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Susitna-Watana Hydroelectric Project Document
ARLIS Uniform Cover Page
Title:
Susitna-Watana Hydroelectric Project, FERC Project no. 14241-000
SuWa 87
Author(s) – Personal:
Sara Fisher-Goad
Author(s) – Corporate:
Alaska Energy Authority
AEA-identified category, if specified:
Correspondence
AEA-identified series, if specified:
Series (ARLIS-assigned report number):
Susitna-Watana Hydroelectric Project document number 87
Existing numbers on document:
Published by:
[Anchorage, Alaska : Alaska Energy Authority, 2013]
Date published:
January 7, 2013
Published for:
Kimberly D. Bose
Date or date range of report:
Volume and/or Part numbers:
Final or Draft status, as indicated:
Document type:
Letter
Pagination:
9, [161] p.
Related work(s):
This letter is a reply to: SuWa 86.
This letter has a response: SuWa 88.
Pages added/changed by ARLIS:
Notes:
With four attachments
All reports in the Susitna-Watana Hydroelectric Project Document series include an ARLIS-
produced cover page and an ARLIS-assigned number for uniformity and citability. All reports
are posted online at http://www.arlis.org/resources/susitna-watana/
1
January 7,2013
The Honorable Kimberly D. Bose
Secretary
Federal Energy Regulatory Commission
888 First Street, NE
Washington, DC 20426
Re:Susitna-Watana Hydroelectric Project, FERC Project No. 14241-000
Dear Secretary Bose:
This responds to the Federal Energy Regulatory Commission (Commission)
Staff’s December 31, 2012, letter to the Alaska Energy Authority (AEA) regarding the
Revised Study Plan (RSP) for the referenced Project filed by AEA on December 14,
2012.
The December 31 letter states that 13 of the 58 study plans “lack sufficient detail”
for the Commission to make a study plan determination (SPD). The Staff’s letter appears
to be based on concerns with the RSP identified in a letter filed by the National Marine
Fisheries Service (NMFS) dated January 2, 2013.1 As explained below, AEA disagrees
with this characterization and requests that the Commission issue the SPD for the entire
RSP under the Integrated Licensing Process (ILP)schedule previously established by the
Commission. If the Commission denies this request, AEA proposes an alternative
schedule which provides SPDs for the 13 studies to be made by April 1, 2013.
I.Background and Context
The Staff’s December 31 letter states that 45 of the 58 study plans contain
sufficient information for the Commission to make an SPD by the currently scheduled
date of February 1, 2013, but that 13 of the plans, which are related to aquatic resources,
do not include sufficient detail for the Commission to make an SPD at this time. Despite
the fact that the 13 study plans total over 850 pages of detailed description, rationale,and
methodology developed over a period of many months’ collaboration with federal and
state resource agencies, Commission staff,and other participants, the letter asserts that
the studies provide only “conceptual details”regarding sampling methods, techniques,
analyt ical approaches, and study site selection.
1 AEA understands that NMFS communicated these concerns in a telephone call to Commission Staff
prior to the December 31 letter. However, NMFS’s January 2 letter, similar to Staff’s December 31 letter,
contains no detailed criticism or analysis of the RSP but only broad-brush, conclusory statements. NMFS’s
January 2 letter provides no basis or justification for altering the SPD schedule.
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Based on the Staff’s conclusory finding, the December 31 letter modifies the SPD
schedule for those 13 studies. It requires AEA to file by March 15, 2013: (1)
implementation plans described in Sections 9.5.4, 9.6.4,and 9.8.4; and (2) final sampling
site selections in “focus areas”for all other studies to be implemented in the middle and
lower Susitna River.The letter also requires AEA to file by January 21, 2013, the results
of open-water flow routing and initial habitat mapping studies conducted in 2012, and to
hold a meeting with stakeholders no later than February 15, 2013, to discuss all of the
above matters. Finally, the letter sets back the schedule for all 13 aquatic studies to
provide for an SPD on May 14, 2013.
Since the beginning of the ILP one year ago, AEA has worked diligently with the
Commission Staff, federal and state agencies, and other licensing participants to identify
needed studies and develop and refine detailed study plans. As described in the RSP filed
on December 14, 2012, at Section 1.1, AEA has undertaken extensive collaborative
efforts for study plan development that exceed the requirements of the Commission’s ILP
regulations in order to ensure that the study plans are robust and comprehensive, and to
ensure broad participation of agencies and other participants. Indeed, with 58 studies
covering approximately 3,500 pages, the Susitna-Watana RSP is likely the most detailed,
comprehensive study plan ever submitted in a hydroelectric licensing proceeding.
For the reasons discussed in detail below, AEA strongly believes that the
Commission’s SPD for the entire RSP can and should be made under the previously
established schedule for all studies in the RSP. More importantly, AEA is extremely
concerned that Staff’s revised SPD schedule for the 13 aquatic studies may cause AEA to
miss the entire 2013 field season for these studies. That would, in effect, set the license
proceeding back a full year. AEA therefore requests that the Commission withdraw the
Staff’s December 31 letter and restore the previous schedule for issuing an SPD for the
entire RSP. If the Commission believes additional information is needed prior to issuing
its SPD on these 13 aquatic studies, AEA proposes an alternative schedule set forth in
Appendix C that preserves the 2013 field season by providing for the SPD for these 13
studies to be made by April 1, 2013.
AEA addresses each of the matters raised by Staff’s December 31 letter below.
II.Implementation Plans
AEA is surprised by Staff’s conclusion that SPDs cannot be made in the absence
of finalized study implementation plans for certain studies. That conclusion is
inconsistent with the Commission’s practice of issuing SPDs for study plans that
contemplate future decisions and adjustments to be made during the study
implementation phase. It is more surprising in this instance, because (as explained
below) Commission Staff, in its recent comments on AEA’s Proposed Study Plan (PSP),
addressed this very issue and provided instructions on how future decisions and
adjustments should be addressed in the RSP—instructions that AEA strictly adhered to
when developing the RSP.
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The three study plans in question are:
RSP 9.5 –Study of Fish Distribution and Abundance in the Upper Susitna River
RSP 9.6 –Study of Fish Distribution and Abundance in the Middle and Lower
Susitna River;and
RSP 9.8 –River Productivity.2
Fish Distribution and Abundance (RSP 9.5 and 9.6)
RSP 9.5 and 9.6 include: goals and objectives; comprehensive reviews of existing
information; identification of study areas; and a description of how each study relates to
other studies. Of signal importance here, they include a great deal of additional
information requested by NMFS, U.S. Fish and Wildlife Service,Commission Staff, and
the Alaska State agencies regarding site selection, sampling stratification, frequency and
schedule, equipment specifications, identification of sampling protocols, and gear
specificity b y habitat.3 The methodologies requested by the agencies have been
substantially incorporated into the plans.4 The plans were developed by highly qualified
fisheries and aquatic biologists in collaboration with the Fish and Aquatic Technical
Working Group (TWG)and are consistent with generally accepted scientific practice.
The only remaining components of these study plans are the implementation
plans, which have the limited purpose of establishing protocols for: (i)identifying
specific sampling locations within the study areas, (ii) sampling techniques and
apparatuses, and (iii) recording the collected data. In November 2012 comments on the
PSP, Commission Staff recognized the reality that certain elements of study plans, such
as these, may need to be modified at a later time—such as once preliminary baseline
studies are complete:
In multiple study plans, you propose to modify the methods or geographic
scope of the study in response to preliminary study results.... For each of
these studies, the RSP should clearly describe any decision-making
process or schedule by which study methods would be refined or adapted
in consultation with agencies and other stakeholders during the study
implementation period, including any criteria that will trigger changes in
the study plan. 5
2 The study plans are attached to this letter in Attachment B. Excerpts from the NMFS and U.S.Fish and
Wildlife Service crosswalk tables documenting AEA’s responses to these agencies’ comments on RSP 9.5,
9.6, and 9.8 are included as Attachment C.
3 See RSP 9.5 and RSP 9.6; RSP Appendix 3, Comment Response Table of Informal Consultation (July –
November 2012).
4 See Attachment C, Crosswalk Tables Between U.S. Fish and Wildlife Service and National Marine
Fisheries Service Study Requests (May 31, 2012) and Alaska Energy Authority Revised Study Plan
(December 14, 2102), filed December 14, 2012, in Project No. 14241.
5 See Letter to Wayne Dyok, AEA, from Dr. Jennifer Hill, Chief, Northwest Branch, Division of
Hydropower Licensing (issued Nov. 14, 2012) (FERC PSP Comments) at A-2.
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The RSP faithfully adheres to this direction. RSP 9.5 and 9.6 state that the Fish
Distribution and Abundance Implementation Plans will include the following
components:
summarize relevant fisheries and an overview of the life history needs for fish
species known to occur in the Susitna River to guide site selection and sampling
protocols,
review the preliminary results of habitat characterization and mapping efforts;
describe site selection and sampling protocols;
develop field data collection forms;
develop database templates that comply with AEA’s quality assurance procedures;
and
develop a protocol for randomizing sampling events to evaluate precision by
habitat and gear type.6
These detailed implementation plans, particularly the location of specific
sampling sites,could not be submitted with the rest of the RSP in December 2012
because fish sampling relies on a stratified random design of sampling by habitat types
(that is, a random sampling component of mesohabitats within each focus area), and
habitat typing. Although selection of specific sampling locations is not complete, the
RSPs do lay out in great detail the methods that will be used to select those sites within
systematically stratified habitats, as shown in the attachments.
River Productivity Study (9.8)
Like the fish distribution and abundance study plans, the river productivity study
plan includes: a statement of goals and objectives, identification of the study area (not in
dispute), discussion of existing and necessary additional data, and extensive discussion of
study and sampling methods.7 As with the other study plans, this plan was developed
through extensive collaboration with the Fish and Aquatic TWG. The bulk of what
remains to be completed is selection of sampling sites, timing, devices,and data
processing. RSP 9.8 also adheres faithfully to Commission Staff’s PSP comments to
describe the decision-making process and schedule to accomplish these things during the
implementation period. The implementation plan will:
summarize relevant macroinvertebrate and algal studies;
provide an overview of target species life-histories;
review the preliminary results of habitat characterization and mapping efforts
and the selected focus areas;
describe site selection, sampling techniques and apparatus, and sample
processing protocols;
6 RSP 9.5, Section 9.5.4., Study Methods, at 9-9 and 9-10; RSP 9.6, Section 9.6.4, at 9-41and 9-42.
7 See RSP Section 9.8.
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include specific sampling locations;
discuss data analysis methods;
develop field data collection forms; and
develop database templates.8
In sum, there is no reason the Commission cannot issue SPDs for these study plans
which, consistent with current practice, allows the details of sampling site locations,
techniques, and protocols to be developed in a cooperative manner during the plan
implementation phase.
III.Final Selection of Focus Area Sampling Sites for All Middle and Lower River
Studies
The PSP proposed, and the RSP includes, 10 Focus Areas in the Middle Susitna
River (Attachment D).9 These are areas from 0.5 to 1.8 miles long identified by aerial
imagery and selected in the context of TWG discussion for intensive study across
resource disciplines. This will assist development of an overall understanding of
interrelationships of river flow dynamics with the physical, chemical, and biological
factors that influence fish habitat.
Consistent with the Commission’s ILP regulations10 and pursuant to the direction
provided in the Commission’s PSP comment letter, AEA’s comprehensive study plans
address (and substantially adopt) the study plans and study plan components proposed by
licensing participants and Commission Staff. In particular, Staff’s PSP comments
requested AEA to include in the RSP with respect to the Focus Areas, the “criteria to be
used for selecting focus areas and study-specific rationale for co-locating sites.”11 Staff
explained, for example:
[Y]ou propose to sample a total of 40 different habitat types (i.e., 8 each of
5 different habitat types: side slough, upland slough, side channel,beaver
complex, and tributary mouth habitat types) within the 10 proposed
Middle River focus areas. However, you do not describe how you will
select these sites within the focus areas. In your RSP, please describe how
these habitat units will be selected within the ten focus areas.12
The RSP faithfully describes the criteria and process for identifying the specific
sampling sites within each Focus Area during the implementation phase, following the
Commission’s SPD. Yet, Staff’s December 31 letter inexplicably changes course by
8 RSP Section 9.8.4 at 9-110 and 9-111.
9 The ten focus areas are fully discussed in the Instream Flow Study Plan in Section 8.5.4.2.1.2.
10 18 C.F.R. §5.13(a).
11 FERC PSP Comments at A-3.
12 Id.at A-12 (emphasis added).
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requiring AEA to complete selection of all sampling sites within the Focus Areas for
these study plans prior to study implementation and the Commission’s SPD.
AEA submits that the Commission should not depart from its established practice
and the previous guidance provided to AEA. In order to assist the Commission’s
consideration of this matter, AEA describes below the Focus Area concept in more detail.
The Susitna River was stratified into geomorphic reaches based on channel type,
gradient, confinement, bed material and tributary confluences in order to characterize the
existing and proposed flow regimes and riverine habitats and organisms. The pros and
cons of various approaches to study site selection,including representative: (i)reach/site
selection;(ii)random reach/site selection;and (iii)critical area/site selection, are
presented in RSP 8.5 (Instream Flow Study).
The concept of Focus Areas was developed in the TWG. AEA has conferred with
the TWG repeatedly concerning the specific location of the Focus Areas. The concept
combines all three of the selection methods noted above because: (i) the areas will
contain habitat types representative of other areas; (ii) the areas will include certain
habitat types repeatedly used by fish and therefore can be considered “critical;”and (iii)
sampling of certain habitat features or mesohabitat types within the areas would be best
approached via random sampling.
The 10 Focus Areas in the Middle Susitna River were discussed by the TWG and
are proposed for detailed study across multiple resource disciplines, as discussed below.
The Focus Areas encompass portions of the main channel, associated side channels,
tributary mouths, side sloughs and upland sloughs.Confirmation of their representative
nature will be determined though the habitat mapping studies conducted in 2012 and
expanded in 2013. If habitat mapping indicates that some key habitat features are not
represented in the proposed areas, additional sampling areas will be identified and studied
in 2014. In addition, some habitat features within the proposed Focus Areas may be
given greater consideration (i.e., weighting) if biological studies in 2013 and 2014
indicate that those habitats features are critical to species productivity.
The study program is not limited to the boundaries of the Focus Areas. Many
other study sites and areas have already been or will be located in the resource specific
investigations (e.g., RSP 8.5, which identifies 80 Middle River and 8 Lower River
transects, most of which are outside the Focus Areas. See also RSPs 5.0, 6.0, 7.5, 7.6,
9.6, 9.8 and 9.9).
Selection of specific sampling sites within the Focus Areas is not necessary for
the Commission to make an SPD for these aquatic studies. As explained above, and as
shown on Attachment D, the Focus Areas are necessarily, indeed intentionally, limited in
size, so the habitat units to be sampled within the Focus Areas have already been
bounded with reasonable certainty. Whether habitat units will be sampled or subsampled
will depend on unit size as determined in the field. In many cases, the most appropriate
sampling sites (e.g., riffle A v. riffle B or C), including biological and field worker safety
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considerations, cannot be identified until ice out and with specific reference to conditions
in the river at the time of sampling.
Finalization of sampling sites within the Focus Areas is particularly unnecessary
for the SPD in the case of the three water quality studies (Baseline Water Quality (5.5),
Water Quality Modeling (5.6), and Mercury Assessment and Potential for
Bioaccumulation (5.7))and the Ice Processes study (7.6). The water quality study Focus
Areas are within the large-scale program both for sampling, but are independent of the
large-scale program both for sampling and for water quality monitoring. Likewise, the
water quality model calibration and operation will be conducted independently of the
Focus Areas. The modeling in the Focus Areas will concentrate on influences of riverine
and reservoir changes on fisheries, while the large scale monitoring program will address
other aspects of water quality. Mercury studies in the Focus Areas are not needed to
evaluate impacts on the river; rather, they are designed to supplement other studies in
Focus Areas.
In sum, there is no reason that issuance of a SPD must await final selection of
sampling sites within the Focus Areas.
IV.Proposed Schedule
The schedule in Staff’s December 31 letter establishes an SPD date for the 13
studies of May 14, 2013. With respect, this is too late to ensure that all 2013 studies are
conducted under a Commission-approved plan. The field study season in Alaska is short.
For many studies (e.g., fish distribution and abundance,instream flow, water quality,ice
processes, groundwater monitoring, river productivity,geomorphology, and fluvial
geomorphology)the sampling period must begin shortly after ice out (generally in April)
and during spring snowmelt flow events. A significant amount of effort and lead time,2-
3 months, is necessary for planning, equipment procurement, fabrication, and installation.
Thus, AEA requests that the Commission reestablish February 1 as the SPD date for all
58 of the RSP study plans.
If the Commission continues to believe that additional information and review
time are needed to issue its SPD on the 13 aquatic studies, 13 AEA proposes an alternative
schedule that will enable the SPD for the 13 aquatic studies to be issued by April 1, 2013
(Attachment A). This would allow AEA to timely complete the necessary prerequisites
to field studies for the 2013 study season.
13 AEA recognizes that the original SPD schedule of February 1 would require comments on the RSP by
licensing participants to be filed by January 18, and that some accommodation might need to be made in
light of the fact that participants now believe they have until April 15 to file comments on the 13 aquatic
studies. Nonetheless, AEA notes that NMFS in its January 2 letter states that it is prepared to file detailed
comments on the RSP by January 18.
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AEA’s proposed schedule would modify Staff’s schedule in the December 31 letter as
follows:
AEA files open-water flow routing model and habitat mapping 2012 study results
on January 31 instead of January 21.As indicated in the schedule presented in the
RSP (Table 8.5-14), AEA intended to present the Middle River habitat mapping
results and the verified open-water flow routing model results in February 2013.
In response to Staff’s request, AEA will complete and file the analysis by January
31. Data collection for the open-water flow routing model was suspended for
safety reasons as a result of the September 2012 Susitna River flood. AEA
resurveyed several cross sections after the flood to ensure that any bathym etry
changes resulting from the flood are incorporated into the model.
AEA posts draft implementation plans for RSP 9.5, 9.6, and 9.8 and final site
selection for Focus Areas for Middle River studies on the Project website on
January 31.
AEA hosts a two-day meeting on February 14 and 15 to discuss the open-water
flow routing model and Middle River habitat mapping results, the selected Middle
River Focus Area sampling sites, the sampling strategy in the Middle Riverfor
each of the 13 studies identified in the December 31 letter, and the two proposed
implementation plans.
AEA files final implementation plans for RSP 9.5, 9.6, and 9.8 and final sampling
sites within focus areas for all 13 studies on March 1 instead of March 15.
Consistent with ILP regulations, licensing participants submit comments on all 13
studies by March 18 (instead of April 14)—15 days following AEA’s submission
of the implementation plans.14
Consistent with ILP regulations, the Commission issues its SPD for RSP 9.5, 9.6,
and 9.8 by April 1(instead of May 14)—30 days following AEA’s submission of
the implementation plans.15
This proposed schedule modifies the amount of time from Staff’s December 31
letter for comment on the study plans and for the Commission to issue its SPD.
However, that is counterbalanced by the facts that:1) Staff’s December 31 letter is
inconsistent with direction given to AEA in Staff’s PSP comments; 2) few studies are
involved;3) the actions Staff has identified as remaining to be done are limited to a small
part of those study plans; 4) the location of the specific sites are reasonably bounded by
the Focus Areas; 5) many final sampling sites cannot be determined except with
reference to conditions at the site and at the time of sampling; 6)the comments will be
informed by the opportunity for participants to meet and discuss the relevant submittals at
the February 14-15 meeting;and 6)there is an urgent need for timely study plan
determinations in order not to miss the 2013 field season.16
14 See 18 C.F.R. §5.13(b).
15 See id.§5.13(c).
16 In light of these facts, it is unclear why Staff’s December 31 letter would double the amounts of time
provided in the ILP regulations for participants to comment on RSPs and for Staff to issue the SPD for the
entire study plan, particularly when only a minor portion of the complete plan is involved.
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V.Other Matters
The schedule attached to the December 31 letter includes a date for filing “[a]ny
study disputes due for studies 5.5, 5.6, 5.7, 6.5, 6.6, 7.5, 7.6, 8.5, 8.6, 9.5, 9.6, 9.8, and
9.9.” AEA seeks clarification from the Commission that by specifically identifying these
studies,the Commission has not made an a priori determination that the identified studies
“pertain directly to the exercise of” the authorities of NMFS under Federal Power Act
(FPA) Section 18 to prescribe fishways or the U.S. Bureau of Land Management (BLM)
to require mandatory license conditions under FPA Section 4(e).17 AEA reserves the
right to contest any assertion that any particular study is directly related to the exercise by
an agency of its relevant authorities.
VI.Conclusion
For the reasons discussed above, AEA requests that the Commission withdraw its
December 31, 2012, letter modifying the ILP schedule and proceed toward issuance of
study plan determinations under the previous schedule. If the Commission continues to
believe that additional information is needed to resolve concerns related to the 13 aquatic
studies, AEA requests that the Commission modify the schedule set forth in the
December 31 letter for the identified study plans and adopt instead the schedule that is
Attachment A to this letter.
If you have questions concerning this matter please contact AEA’s Project
Manager, Wayne Dyok, at wdyok@aidea.org or (907) 771-3955.
Sincerely,
Sara Fisher-Goad
Executive Director
Alaska Energy Authority
Attachments
Cc: Distribution List
Jeff Wright
Ann Miles
Vince Yearick
Dr. Jennifer Hill
David Turner
17 See 18 C.F.R. § 5.14(a).
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Attachment A
AEA Proposed Alternative Study Plan Determination Schedule
For Aquatic Studies
Responsible
Party Pre-Filing Milestone Current Date AEA Proposed Date
AEA AEA files results of open-water flow routing
model and habitat mapping.
January 21,
2013
January 31, 2013
AEA AEA provides to FERC and licensing
participants:
results of open-water flow routing
model;
habitat mapping;
DRAFT Fish Distribution and
Abundance Implementation Plan;
DRAFT River Productivity
Implementation Plan;
Description of habitat units within the
Focus Area for all aquatic studies to be
implemented in the Middle a River.
January 31, 2013
AEA and
All
Stakeholders
Discuss study results, draft implementation
plans, and site selection for all studies to be
implemented in the Middle and Lower Susitna
River.
February 15,
2013
February 14-15, 2013
AEA AEA files studies 9.5 and 9.6, Fish Distribution
and Abundance Implementation Plan; study 9.8,
River Productivity Implementation Plan; and
describes habitat units within the Focus Areas in
studies 5.5, 5.6, 5.7, 6.5, 6.6, 7.5, 7.6, 8.5, 8.6,
9.6, 9.8, and 9.9 that will be sampled or
subsampled depending on the size of the habitat
unit, as determined in the field.
March 15, 2013 March 1, 2013
All
Stakeholders
Revised Study Plan Comments Due for studies
5.5, 5.6, 5.7, 6.5, 6.6, 7.5, 7.6, 8.5, 8.6, 9.5, 9.6,
9.8, and 9.9.
April 14, 2013 March 18, 20131
FERC Director’s Study Plan Determination for studies
5.5, 5.6, 5.7, 6.5, 6.6, 7.5, 7.6, 8.5, 8.6, 9.5, 9.6,
9.8, and 9.9.
May 14, 2013 April 1, 2013
1 The 15 day response time for RSP comments and the 30 day time for issuance of an SPD fall on weekends.
Therefore, the proposed comment dates for both are the next business day.
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ATTACHMENT B
Revised Study Plans
RSP 9.5 (Fish Distribution and Abundance in the Upper Susitna River)
RSP 9.6 (Fish Distribution and Abundance in the Lower and Middle Susitna River)
RSP 9.8 (River Productivity)
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REVISED STUDY PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9-6 December 2012
9.5. Study of Fish Distribution and Abundance in the Upper Susitna
River
9.5.1. General Description of the Proposed Study
This study is focused on describing the current fish assemblage including spatial and temporal
distribution, and relative abundance by species and life stage in the Susitna River upstream of the
proposed Watana Dam (RM 184). Fishery resources in the upper sections of the Susitna River
basin consist of a variety of salmonid and non-salmonid resident fish (Table 9.5-1). With one
known exception (i.e., Chinook salmon), existing information indicates that anadromous fish are
restricted to the mainstem Susitna River and tributaries downstream of Devils Canyon near RM
150 due to their apparent inability to pass several steep rapids. In addition to investigating the
resident salmonid and non-salmonid fishes present in this part of the river, this study will also
investigate the distribution and abundance of any anadromous fish above the proposed Watana
Dam site. Chinook salmon have been observed in relatively low numbers above Devils Canyon
(maximum peak count of 46 adult Chinook salmon during 1984; Thompson et al. 1986).
The physical habitat modeling efforts proposed in the Fish and Aquatics Instream Flow Study
(Section 8.5) require information on the distribution and periodicity of different life stages for
the fish species of interest. Not all life stages of the target fish species may be present
throughout the Upper Susitna River, and seasonal differences may occur in their use of some
habitats. For example, some fish that use tributary streams during the open-water period may
overwinter in mainstem habitats.
This study is designed to provide baseline biological information regarding periodicity and
habitat suitability for the Instream Flow Modeling Study (see Section 8.5). Results of this study
will include key life history information about fish species in the Upper Susitna River, which
will provide inputs for the Study of Fish Barriers in the Middle and Upper Susitna River and
Susitna Tributaries (Section 9.12) and the Study of Fish Passage Feasibility at Watana Dam
(Section 9.11).
Study Goals and Objectives
The overarching goal of this study is to characterize the current distribution, relative abundance,
run timing, and life history of resident and non-salmon anadromous species (e.g., Dolly Varden,
humpback whitefish, round whitefish, Arctic grayling, northern pike, and Pacific lamprey), and
freshwater rearing life stages of anadromous fish (fry and juveniles) in the Susitna River above
the proposed dam site (RM 184). Specific objectives include the following:
1. Describe the seasonal distribution, relative abundance (as determined by catch per unit
effort [CPUE], fish density, and counts), and fish-habitat associations of resident fishes,
juvenile anadromous salmonids, and the freshwater life stages of non-salmon
anadromous species.
2. Describe seasonal movements of juvenile salmonids and selected fish species such as
rainbow trout, Dolly Varden, humpback whitefish, round whitefish, northern pike, Pacific
lamprey, Arctic grayling and burbot within the hydrologic zone of influence upstream of
the Project.
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REVISED STUDY PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9-7 December 2012
a. Document the timing of downstream movement and catch using out-migrant
traps.
b. Describe seasonal movements using biotelemetry (passive integrated transponders
[PIT] and radio-tags).
c. Describe juvenile Chinook salmon movements.
3. Characterize the seasonal age class structure, growth, and condition of juvenile
anadromous and resident fish by habitat type.
4. Determine whether Dolly Varden and humpback whitefish residing in the Upper River
exhibit anadromous or resident life histories.
5. Determine baseline metal concentrations in fish tissues for resident fish species in the
mainstem Susitna River (see Section 5.5 Water Quality and Section 5.7, Mercury
Assessment and Potential for Bioaccumulation Study).
6. Document the seasonal distribution, relative abundance, and habitat associations of
invasive species (northern pike).
7. Collect tissue samples to support the Genetic Baseline Study for Selected Fish Species
(Section 9.14).
9.5.2. Existing Information and Need for Additional Information
Information regarding resident species, non-salmon anadromous species, and the freshwater
rearing life stages of anadromous salmon was collected during studies in connection with Alaska
Power Authority’s (APA’s) proposed Susitna Hydroelectric Project in the 1980s. Existing
information includes the spatial and temporal distribution of fish species and their relative
abundance. The Pre-Application Document (PAD) (AEA 2011a) and Aquatic Resources Data
Gap Analysis (ARDGA; AEA 2011b) summarized this existing information and also identified
data gaps for resident and rearing anadromous fish.
A total of nine anadromous and resident fish species have been documented inhabiting the
Susitna River drainage upstream of Devils Canyon (Table 9.5-1). Chinook salmon use of the
Upper Susitna River was first documented during the 1980s studies; this is the only anadromous
fish documented to pass the rapids at Devils Canyon. Resident species that have been identified
in all three segments of the Susitna River include Arctic grayling, Dolly Varden, humpback
whitefish, round whitefish, burbot, longnose sucker, and sculpin (Schmidt et al. 1985;
Buckwalter 2011). To varying degrees, the relative abundance and distribution of these species
were determined during the early 1980s studies. For most species, the dominant age classes and
sex ratios were also determined, and movements, spawning habitats, and overwintering habitats
were identified for certain species.
One species that has not been documented in the Susitna River, but may occur in the upper
Susitna drainage, is lake trout. Lake trout have been observed in Sally Lake and Deadman Lake
of the upper Susitna watershed (Delaney et al. 1981a) but have not been observed in the
mainstem Susitna or tributary streams. Pacific lamprey have been observed in the Chuit River
(Nemeth et al. 2010), which also drains into Cook Inlet. Northern pike is an introduced species
that has been observed in the Lower and Middle River (Rutz 1999). Although it is considered
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unlikely that Pacific lamprey and northern pike are present in the Upper Susitna River, this study
will be helpful for evaluating these species’ distributions.
In the proposed impoundment zone, Arctic grayling are believed to be the most abundant fish
species (Delaney et al. 1981a; Sautner and Stratton 1983) and were documented spawning in
tributary pools. In tributaries, juvenile grayling were found in side channels, side sloughs, and
pool margins and in the mainstem at tributary mouths and clear water sloughs during early
summer. Dolly Varden populations in the Upper Susitna River are apparently small but widely
distributed. Burbot in the Upper Susitna River were documented in mainstem habitats with
backwater-eddies and gravel substrate. The abundance of longnose suckers in the Upper Susitna
River was less than downstream of Devils Canyon. Specific information needs relative to fish
distribution and abundance in the Upper Susitna River that were identified in the ARDGA (AEA
2011b) include the following:
Population estimates of adult Arctic grayling and Dolly Varden in select tributaries
within the proposed impoundment zone.
The migration timing of Arctic grayling spawning in the proposed impoundment zone,
the relative abundance and distribution of Dolly Varden, lake trout, and juvenile Chinook
salmon in the impoundment zone.
Physical habitat characteristics used by round whitefish, longnose sucker, and burbot
within the impoundment zone.
Little is known about the density and distribution of juvenile salmon in the Susitna River
upstream of Devils Canyon (RM 150) and the proposed dam site at RM 184. All five species of
Pacific salmon were captured in the Lower and Middle Susitna River during the 1980s licensing
studies. Coho, chum, sockeye, and pink salmon have not been observed upstream of the Devils
Canyon rapids. Chinook salmon are the only anadromous species known to occur in the Upper
Susitna River and tributaries although the information on the extent of their distribution is
limited. In 1984, Chinook spawning was documented upstream of Devils Canyon but
downstream of the proposed dam site at Chinook Creek (RM 156.8), and Fog Creek (RM 176.7)
(ADF&G 1985). More recent sampling has documented adults in Fog and Tsusena Creeks (RM
181.3) and upstream of the proposed dam site in Kosina Creek (RM 201). Juvenile Chinook
salmon have been documented recently upstream of Devils Canyon in Fog Creek, and upstream
of the proposed dam site in Kosina Creek, and in the Oshetna River (RM 225) (Buckwalter
2011). Historic data indicate that Susitna River Chinook salmon spawn exclusively in tributary
streams (Thompson et al. 1986;Barrett et al.1983; Barrett 1974, 1985) and that nearly all
Chinook salmon juveniles in this system out-migrate to the ocean as age-1+ fish, and very few
exit the system as fry.
Existing fish and aquatic resource information appears insufficient to address the following
issues that were identified in the PAD (AEA 2011a):
F1: Effect of change from riverine to reservoir lacustrine habitats resulting from Project
development on aquatic habitats, fish distribution, composition, and abundance, including
primary and secondary productivity.
F2: Potential effect of fluctuating reservoir surface elevations on fish access and
movement between the reservoir and its tributaries and habitats.
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F3: Potential effect of Watana Dam on fish movement.
Site-specific knowledge of the distribution, timing, and abundance of fish likely to occupy the
proposed Watana Reservoir primarily depends on the results of surveys conducted by the Alaska
Department of Fish and Game (ADF&G) during the early 1980s using multiple sampling
methods (AEA 2011a). The existing information can provide a starting point for understanding
the distribution and abundance of anadromous and resident freshwater fishes in the Susitna River
and the functional relationship with the habitat types present. However, any significant
differences in the patterns in abundance and distribution observed during the 1980s compared to
current conditions need to be determined.
In addition to providing baseline information about aquatic resources in the proposed Project
area, aspects of this study are designed to complement and support other fish and aquatic studies.
9.5.3. Study Area
The study area encompasses the mainstem Susitna River from the proposed Watana Dam site
(RM 184) upstream to the Oshetna River confluence (RM 233.4) (Figure 9.5-1). The Upper
Susitna River is delineated by the location of the proposed Watana Dam because effects of the
Project are anticipated to be different upstream and downstream of the proposed dam. The
mainstem Susitna River and its tributaries upstream of the proposed dam will be within the
impoundment zone and subject to Project operations that affect daily, seasonal, and annual
changes in pool elevation plus the effects of initial reservoir filling. Tributary surveys upstream
of the proposed Watana Dam are further delineated by the 3,000-foot elevation contour, which is
based on the known extent of juvenile Chinook salmon distribution. Some study components,
such as resident fish life-history studies and juvenile Chinook salmon distribution sampling, may
extend beyond the core area.
9.5.4. Study Methods
This study will employ a variety of field methods to build upon the existing information related
to the distribution and abundance of fish species in the Upper Susitna River. The following
sections provide brief descriptions of study site selection, sampling frequency, the approach, and
suite of methods that will be used to accomplish each objective of this study. This study was
initiated in 2012 and will continue over the next two years to survey as much habitat as possible.
Fish Distribution and Abundance Sampling Plan
Some details of the sampling scheme have been provided for planning purposes; however,
modifications may be appropriate as the results of 2012 data collection are reviewed. A final
sampling scheme will be developed as part of the detailed Fish Distribution and Abundance
Implementation Plan, for Sections 9.5 and 9.6, which will be submitted to FERC no later than
March 15, 2013. Implementation plan development will include (1) a summary of relevant
fisheries and an overview of the life history needs for fish species known to occur in the Susitna
River to guide site selection and sampling protocols, (2) a review of the preliminary results of
habitat characterization and mapping efforts (Section 9.9), (3) a description of site selection and
sampling protocols, (4) development of field data collection forms, and (5) development of
database templates that comply with 2012 AEA QA/QC procedures. The implementation plan
will include the level of detail sufficient to instruct field crews in data collection efforts. In
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addition, the plan will include protocols and a guide to the decision-making process in the form
of a chart or decision tree that will be used in the field, specific sampling locations, details about
the choice and use of sampling techniques and apparatuses, and a list of field equipment needed.
The implementation plan will address how sampling events will be randomized to evaluate
precision by habitat and gear type. The implementation plan will also help ensure that fish
collection efforts occur in a consistent and repeatable fashion across field crews and river
segments. Proposed sampling methods by objective are presented below and in Table 9.5-2.
Brief descriptions of each sampling technique are provided in Section 9.5.4.4.
9.5.4.1 Study Site Selection
The Upper Susitna River will represent an area where the mainstem river will be inundated and
tributaries will be partially altered. As a result, the sampling effort will be tailored to collect
necessary information to document fish assemblages, distribution, and abundance generally
within the mainstem river and more intensely within the tributary habitat inundated up to an
elevation of 2,200 feet. The number of sites may be revisited after sampling in 2013, if Chinook
are located in tributaries above 2,200 feet.
A nested stratified sampling scheme will be used to select study sites to cover the range of
habitat type. The habitat classification hierarchy, as described in Section 9.9.5.4.1 of the Habitat
Classification Study, will be composed of five levels representing (1) major hydraulic segment;
(2) geomorphic reach; (3) mainstem habitat type; (4) main channel mesohabitat; and (5) edge
habitat (Table 9.9-4, Nested and tiered habitat mapping units and categories).
Level 1 will generally identify the Lower River (RM 28-98), Middle River (RM 98-184), and
Upper River (RM 184-233) from each other. The mainstem Susitna River and its tributaries
upstream of the proposed dam will be within the impoundment zone and subject to Project
operations that affect daily, seasonal, and annual changes in pool elevation plus the effects of
initial reservoir filling. In contrast, the mainstem downstream of the Project will be subject to
the effects of flow modification from Project operations, which will diminish below the Three
Rivers Confluence.
Level 2 will identify unique reaches established from the channel’s geomorphic characteristics
(established from the Geomorphology Study [Section 6.0]). The Geomorphic Study Team will
delineate the Lower, Middle, and Upper River segments into large-scale geomorphic river
reaches with relatively homogeneous landform characteristics, including at generally decreasing
scales: geology, hydrology (inflow from major tributaries), slope, channel planform, braiding or
sinuosity index (where relevant), entrenchment ratio, channel width, and substrate size.
Stratification of the river into relatively homogeneous segments will facilitate relatively unbiased
extrapolation of sampled site data within the individual segments because sources of variability
associated with large-scale features will be reduced.
Level 3 classifies the mainstem habitat into main channel, off-channel, and tributary habitat
using an approach similar to the 1980s historical habitat mapping definitions (ADF&G 1983).
The main channel includes five mainstem habitat types, whereas the off-channel habitat will be
categorized into four types (Table 9.9-4). The 1980s classification of riverine habitats of the
Susitna River included six major mainstem habitat categories consisting of main channel, side
channel, side slough, upland slough, tributaries, and tributary mouths (ADF&G 1984). These
mainstem habitat categories will be maintained in the 2012 classification system, but they are
further categorized into main channel, off-channel, and tributary. These will be expanded to
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include five types of main channel (main channel, split main channel, multiple split main
channel, side channel, and tributary), and four types of off-channel (slide slough, upland slough,
backwater, and beaver complex) (Table 9.9-4).
Level 4 will further delineate Level 3 main channel and tributary habitats into mesohabitat types
(pool, riffle, glide, and cascade) (Table 9.9-4). However, off-channel habitat will remain at
Level 3 (side slough, upland slough, backwater, and beaver complex).
The presence, distribution, and frequency of these habitats vary longitudinally within the river
depending in large part on its confinement by adjoining floodplain areas, size, and gradient.
Thus, fish sampling in the Upper River will necessarily vary with habitat and will not be
stratified equally among geomorphic reaches (Level 2). Stratification will occur across
geomorphic reaches as much as possible but will be dictated by the distribution of habitat types
present within each reach. For example, based on preliminary geomorphic reach delineation, we
would expect to find multiple split main channel habitats in reaches UR1 and UR6 but not in the
more confined and incised reaches UR2 through UR5. In order to ensure that representative
habitats are sampled along the Upper River, six replicate sampling sites will be selected within
each Level 3 habitat type for fish distribution sampling (27 sites). In addition, one replicate of
each Level 4 main channel habitat nested within each Level 3 habitat will be selected for relative
abundance sampling (Figure 9.5-2).
Habitat mapping in the tributaries will be completed differently than in the mainstem river due to
the lack of complete aerial imagery, relatively smaller channel size, steep gradient, and limited
on the ground accessibility for direct mapping. Because of this general inaccessibility, very
rugged terrain, and mostly non-wadeable stream channels, near census mapping (100 percent
coverage) is challenging and in some cases unsafe or impossible. For these reasons, only
tributaries mapped by the Characterization and Mapping of Aquatic Habitats Study (Section 9.9;
Table 9.9-2) will be selected for fish distribution and abundance sampling. Up to 18 tributary
streams will be targeted for sampling during 2013 and 2014. All tributaries in which Chinook
salmon juveniles or adults were observed within or at the mouth of a tributary during 2012, or
during previous surveys by Buckwalter (2011) (i.e., Fog Creek, Kosina Creek, Tsusena Creek,
Oshetna River), will be sampled. Of the remaining tributaries that are suitable for sampling
(Table 9.9-2), efforts will be directed towards streams that are not already identified as
supporting anadromous fishes in the ADF&G Anadromous Waters Catalog (AWC). Selected
study sites will comprise a target of 25 percent of the mapped habitats in each tributary; this
target will vary with access considerations. All known Chinook salmon-bearing tributaries will
be sampled up to the 3,000-foot elevation contour, which is based on the known extent of
Chinook salmon distribution.
Site selection includes first completing the geomorphic reach delineation and habitat mapping
tasks. In addition to technical considerations, access and safety will be key non-technical
attributes for site selection for all studies. This, too, influenced site selection in the 1980s
studies, and will certainly influence site selection in the present studies.
9.5.4.2 Sampling Frequency
Sampling frequency will vary among sites based on specific objectives. Generally, sampling
will occur seasonally during the ice-free period. Additional effort, up to bi-weekly sampling,
will be required immediately following ice-out in an attempt to capture critical juvenile Chinook
salmon out-migration from natal tributaries to rearing habitats.
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9.5.4.3 Fish Sampling Approach
The initial task of this study will consist of a focused literature review to guide selection of
appropriate sampling methods by species and habitat type, sampling event timing, and sampling
event frequency. Anticipated products from the literature review include the following:
A synthesis of existing information on life history, spatial and temporal distribution, and
relative abundance by species and life stage.
A review of sampling strategies, methods, and procedures used in the 1980s fish studies.
Preparation of periodicity charts for each species within the study area (timing of adult
migration, holding, and spawning; timing of incubation, rearing, and out-migration).
A summary of mainstem Susitna River habitat utilization for each species, by riverine
habitat type (main channel, side channel, side slough, upland slough, tributary mouth,
tributary).
A summary of existing age, size, and genetics information.
A summary of distribution of invasive species, such as northern pike.
Knowledge of behavior and life history of the target species is essential for effective survey
design. Selected fish sampling techniques will vary based on habitat characteristics, season, and
species/ life history of interest. Timing of surveys depends on the objectives of the study and the
behavior of the target fish species. Since life stage-specific information is desirable, timing of
the survey must match the use of the surveyed habitat by that life stage.
9.5.4.3.1 Objective 1: Fish Distribution, Relative Abundance, and Habitat Associations
Two general approaches to fish sampling will be used. The first is focused on gathering data on
general fish distribution (presence/absence). This sampling involves a single pass with
appropriate gear types. To the extent possible, the selected transects will be standardized and the
methods will be repeated during each sampling event at a specific site to evaluate temporal
changes in fish distribution. The second sampling approach is to gather data on relative
abundance as determined by CPUE and density; complementary data on fish size, age, and
condition factor will also be collected. The selected transects and fish capture methods (i.e.,
number of passes, amount of soak time) will be standardized such that they are repeatable on
subsequent sampling occasions. This approach will also emphasize the identification of foraging
and spawning habitats.
Long daylight hours during the summer may reduce the difference between day and night
sampling effectiveness. The periods of twilight are important sampling periods. Sampling
schedules will encompass daylight, twilight, and evening periods.
Task A: Fish Distribution Surveys
Fish distribution surveys will include seasonal sampling events during the ice-free seasons.
Methods will be selected based on species, life stage, and water conditions. Snorkeling and
electrofishing are preferred methods for juvenile fishes in clear water areas where velocities are
safe for moving about in the creek. The use of minnow traps, beach seines, set nets, and fyke
nets will be employed as alternatives in deeper waters and habitats with limited access, low
visibility, and/or high velocities. For larger/adult fishes, gillnets, seines, trotlines, hoop traps,
and angling will be used.
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Survey methods will likely vary for the different study areas in the Upper Susitna River.
Whereas snorkeling, minnow trapping, backpack electrofishing, and beach seines may be
applicable to sloughs and other slow-moving waters, it is anticipated that gillnetting, boat
electrofishing, hoop traps, and trot lines may be more applicable to the mainstem. The decisions
about what methods to apply will be made by field crews after initial site selection in
coordination with Fish Distribution and Abundance Study Lead and the Fish Program Lead and
in accordance with state and federal fish sampling permit requirements.
Task B: Relative Abundance
Relative abundance surveys will include seasonal multi-pass sampling events during the ice-free
seasons. As mentioned above, methods will be selected based on species, life stage, and water
conditions. All methods will be conducted consistent with generating estimates of CPUE that are
meaningful and facilitate comparison of counts or densities of fish over space and time. This
includes calibration and quality control of methods and documentation of conditions that affect
sampling efficiency—such as visibility, water temperature, and conductivity—to ensure that a
consistent level of effort is applied over the sampling unit.
Task C: Fish-Habitat Associations
In conjunction with Tasks 1 and 2, data will be collected for fish distribution and abundance by
habitat type. This task includes an analysis of fish presence, distribution, and density by
mesohabitat type by season. The information on fish habitat use will help identify species and
life stages potentially vulnerable to Project effects.
9.5.4.3.2 Objective 2: Seasonal Movements
Task A: Document the timing of downstream movement and catch for all fish species using
out-migrant traps.
Understanding the timing of migration from natal tributaries to the mainstem Susitna River and
from the Upper Susitna River to the proposed dam site (RM 184) is important for assessing the
potential effects of the proposed Project. Out-migrant traps (rotary screw traps and inclined
plane traps) are useful for determining the timing of downstream migrating juvenile salmonids
and resident fish.
A maximum of two out-migrant traps will be deployed. In addition to collection of data on
migratory timing, size at migration, and growth, out-migrant traps will also serve as a platform
for tagging juvenile fish (Objective 2, Task C), recapturing previously tagged fish, collecting fish
for stomach contents analysis in support of the River Productivity Study (Section 9.8), and
collecting tissue samples (Objective 7) to support the Genetic Baseline Study for Selected Fish
Species (Section 9.14).
Task B: Describe seasonal movements using biotelemetry.
Biotelemetry techniques will include radio telemetry and PIT technology. PIT tags will be
surgically implanted in small fish >60 mm to monitor movement and growth; radio transmitters
will be surgically implanted in adult fish of sufficient body size of selected species distributed
temporally and longitudinally in the Upper River.
PIT tag antenna arrays with automated data logging will be used at selected side channels and
tributary mouths to detect movement of tagged fish into or out of the site. Recaptured fish will
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provide information on the distance and time travelled since the fish was last handled and
changes in length (growth).
Radio-tagged fish will be tracked with monthly aerial surveys and by boat, in conjunction with
the Salmon Escapement Study (Section 9.7) to describe seasonal movements of selected fish
species with emphasis on identifying spawning and overwintering habitats within the hydrologic
zone of influence upstream of the Project.
Up to 30 radio transmitters will be implanted in selected species including Arctic grayling, Dolly
Varden, burbot, round whitefish, humpback whitefish, and northern pike if present (Objective 6).
A PIT tag will be implanted into up to 1,000 fish of these species per PIT tag array that are in
close proximity to an array and approximately 60 mm and larger.
Task C: Describe juvenile Chinook salmon movements.
Juvenile Chinook salmon movement within the Upper River will be described using out-migrant
traps and biotelemetry methods outlined in Objective 2, Tasks A and B. This study proposes to
implant PIT tags in all juvenile Chinook salmon >60 mm in length to document seasonal
movement within the Upper River using antenna arrays placed in tributary mouths, sloughs, and
side channels and on out-migrant traps to recapture fish. Because of the low number of adult
Chinook salmon tracked to the Upper River with radio-tags in 2012, all juvenile Chinook salmon
of taggable size need to be tagged to obtain a sufficient sample size. Out-migrant traps will be
used to document juvenile Chinook salmon migratory timing and size at migration from natal
tributaries to the Upper River and out-migration from the Upper River to below the proposed
dam site (RM 184). The data on juvenile Chinook salmon movement patterns and timing will
support the Study of Fish Passage Feasibility at Watana Dam (Section 9.11).
9.5.4.3.3 Objective 3: Characterize the seasonal age class structure, growth, and condition
of juvenile anadromous and resident fish by habitat type.
In conjunction with Objectives 1 and 2, all captured fish will be identified to species, measured
to the nearest millimeter (mm) fork length, and weighed to the nearest gram. Length frequency
data by species will be compared to length-at-age data in the literature to infer age classes.
Recaptured PIT-tagged fish (Objective 2, Task B) will provide information on changes in length
and weight (growth). Recorded parameters in each habitat unit will include number of fish by
species and life stage, fork length, global positioning system (GPS) location of sampling area,
time of sampling, weather conditions, water temperature, water transparency, behavior, and
location and distribution of observations.
9.5.4.3.4 Objective 4: Determine whether Dolly Varden and humpback whitefish residing in
the Upper River exhibit anadromous or resident life histories.
Otoliths will be collected from Dolly Varden and humpback whitefish greater than 200 mm (7.8
inches) in length to test for marine-derived elements indicative of an anadromous life history
pattern. It is assumed that larger fish are more likely to have exhibited anadromy and therefore
otolith collection is proposed only from fish greater than 200 mm in length. A target of 30 fish
of each species during 2013 and 2014 will be collected (60 fish of each species total).
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9.5.4.3.5 Objective 5: Determine baseline metal and mercury concentrations in fish tissues
for resident fish species in the mainstem Susitna River.
Tissue or whole fish samples will also be collected in the mainstem Susitna River for assessment
of metals (see Section 5.5.4.7, Baseline Metal Levels in Fish Tissue) and mercury (see Section
5.7.4.2.6, Mercury Assessment and Potential for Bioaccumulation Study) concentrations. Target
fish species for baseline metals testing include: Dolly Varden, Arctic grayling, whitefish species,
long nose sucker, lake trout, burbot, and resident rainbow trout. Target fish species for mercury
sampling include: Dolly Varden, arctic grayling, stickleback, long nose sucker, whitefish species,
lake trout, burbot, and resident rainbow trout.
9.5.4.3.6 Objective 6: Document the seasonal distribution, relative abundance, and habitat
associations of invasive species (northern pike).
Northern pike were likely established in the Susitna River drainage in the 1950s through a series
of illegal introductions (Rutz 1999). The proliferation of this predatory species is of concern
owing to its effect on salmonids and other species such as stickleback. At this time, northern
pike have not been documented in the Upper River, so no targeted collection effort for pike will
be made. However, the presence/absence and habitat associations of northern pike and other
invasive fish species will be documented as a component of all fish capture and observation
sampling events associated with Objectives 1 and 2.
9.5.4.3.7 Objective 7: Collect tissue samples from juvenile salmon and all resident and non-
salmon anadromous fish.
In support of the Genetic Baseline Study for Selected Fish Species (Section 9.14), fish tissues
will be collected opportunistically in conjunction with all fish capture events. The target number
of samples, species of interest, and protocols are outlined in Section 9.14. Tissue samples
include an axillary process from all adult salmon, caudal fin clips from fish >60 mm, and whole
fish <60 mm.
9.5.4.4 Fish Sampling Techniques
A combination of gillnetting, electrofishing, angling, trot lines, minnow traps, snorkeling, out-
migrant trapping, beach seines, fyke nets, hoop nets, dual-frequency identification sonar
(DIDSON), and underwater video camera techniques will be used to sample or observe fish in
the Upper River, and moving in and out of selected sloughs and tributaries draining to the
Susitna River. Several assumptions are associated with the use of the proposed methods:
If it can be conducted safely, snorkeling, electrofishing, and gillnetting will require
nighttime sampling in clear-water areas to increase the efficacy of fish capture or
observation.
Gillnetting is likely the most effective means of capturing fish in open-water areas of the
main Susitna River channel.
All fish sampling and handling techniques described within this study will be conducted
under state and federal biological collection permits. Limitations on the use of some
methods during particular time periods or locations may affect the ability to make
statistical comparisons among spatial and temporal strata.
Fish sampling techniques provide imperfect estimates of habitat use and relative fish
abundance. Use and comparison of multiple sampling methods provides the opportunity
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to identify potential biases, highlight strengths and weaknesses of each method, and
ultimately improve estimates of fish distribution and relative abundance.
Sampling in the reservoir inundation zone will be scaled based on elevation and Chinook
salmon distribution. More intensive surveys will be conducted in tributaries to be
inundated up to an elevation of 2,200 feet. Sampling from 2,200 feet to 3,000 feet
elevation will be focused on Chinook salmon. If Chinook salmon are located, sub-
sampling will continue upstream to the upper extent of suitable Chinook salmon habitat.
9.5.4.4.1 Gillnet Sampling
Variable mesh gillnets (7.5-foot-deep panels with 1-inch to 2.5-inch stretched mesh) will be
deployed. In open water and at sites with high water velocity, gillnets will be deployed as drift
nets, while in slow water sloughs, gillnets will be deployed as set (fixed) nets. The location of
each gillnet set will be mapped using hand-held GPS units and marked on high-resolution aerial
photographs. The length, number of panels, and mesh of the gillnets will be consistent with nets
used by ADF&G to sample the river in the 1980s (ADF&G 1982, 1983, 1984). To reduce
variability among sites, soak times for drift gillnets will be standardized; all nets will be retrieved
a maximum of 30 minutes after the set is completed. The following formula will be used to
determine drifting time:
T = ([(set time + retrieval time)/2] + soak time)
9.5.4.4.2 Electrofishing
Boat-mounted, barge, or backpack electrofishing surveys will be conducted using standardized
transects. Boat-mounted electrofishing is the most effective means of capturing fish in shallow
areas (<10 feet deep) near stream banks and within larger side channels. Barge-mounted
electrofishing is effective in areas that are wadeable, but have relatively large areas to cover and
are too shallow or otherwise inaccessible to a boat-mounted system. Backpack electrofishing is
effective in wadeable areas that are relatively narrow. The effectiveness of barge and backpack
electrofishing systems can be enhanced through the use of block nets. Electrofishing methods
will follow NMFS (2000) Guidelines for Electrofishing Waters Containing Salmonids Listed
Under the Endangered Species Act.
Sites will be selected carefully, because electrofishing may have limited success in swift, turbid,
or low conductivity waters. Suspended materials in turbid water can affect conductivity, which
may result in harmful effects on fish, especially larger fish due to a larger body surface in contact
with the electrical field. Sudden changes in turbidity can create zones of higher amperage, which
can be fatal to young-of-year fish as well as larger fish. Electrofishing in swift current is
problematic, with fish being swept away before they can be netted. Similarly, turbidity increases
losses from samples. Electrofishing will be discontinued immediately in a sampling reach if
large salmonids or resident fish are encountered.
Selection of the appropriate electrofishing system will be made as part of site selection, which
will include a site reconnaissance. In all cases, the electrofishing unit will be operated and
configured with settings consistent with guidelines established by Smith Root. The location of
each electrofishing transect will be mapped using hand-held GPS units and marked on high-
resolution aerial photographs. To the extent possible, the selected electrofishing system and
transects will be standardized and the methods will be repeated during each sampling period at a
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specific site to evaluate temporal changes in fish distribution. Habitat measurements will be
collected at each site using the characterization methods identified in Section 9.9. Any changes
will be noted between sample periods. The electrofishing start and stop times and water
conductivity will be recorded. Where safety concerns can be adequately addressed,
electrofishing will also be conducted after sunset in clear water areas; otherwise, electrofishing
surveys will be conducted during daylight hours.
9.5.4.4.3 Angling
Angling with hook and line can also be an effective way to collect fish samples depending on the
target species. During field trips organized for other sampling methods, hook-and-line angling
will be conducted on an opportunistic basis using artificial lures or flies with single barbless
hooks. The primary objective of hook-and-line sampling will be to capture subject fish for
tagging (e.g., northern pike) and to determine presence/absence; a secondary objective will be to
evaluate seasonal fish distribution. Because it is labor and time intensive, angling is best used as
an alternative method if other more effective means of sampling are not available. Angling can
also be used in conjunction with other methods, particularly if information is required on the
presence and size of adult fish.
9.5.4.4.4 Trot Lines
Trot lines can be an effective method for capturing burbot, rainbow trout, Dolly Varden,
grayling, and whitefish. Trotlines are typically a long line with a multitude of baited hooks and
are typically anchored at both ends and set in the water for a period of time. Trot line sampling
was one of the more frequently used methods during the 1980s and was the primary method for
capturing burbot; however, trot lines are generally lethal. Trot lines will consist of 14 to 21 feet
of seine twine with six leaders and hooks lowered to the river bottom. Trot lines will be checked
and rebaited after 24 hours and pulled after 48 hours. Hooks will be baited with salmon eggs,
herring, or whitefish. Salmon eggs are usually effective for salmonids, whereas herring or
whitefish are effective for burbot. Trot line construction and deployment will follow the
techniques used during the 1980s studies as described by ADF&G (1982). As per ADF&G Fish
Resource Permit stipulations, all salmon eggs used as bait will be commercially sterilized or
disinfected with a 10-minute soak in a 1/100 Betadyne solution prior to use.
9.5.4.4.5 Minnow Traps
Minnow traps baited with salmon eggs are an effective method for passive capture of juvenile
salmonids in pools and slow-moving water (Bryant 2000). In reaches where both electrofishing
and snorkeling would be ineffective due to stream conditions such as deep, fast water, baited
minnow traps will be used as an alternative to determine fish presence. During the 1980s,
minnow traps were the primary method used for capturing sculpin, lamprey, and threespine
stickleback. Minnow traps also captured rainbow trout and Arctic grayling. Minnow traps will
be baited with salmon roe, checked, and rebaited after 90 minutes following protocols outlined
by Bryant (2000). Between 5 and 10 minnow traps will be deployed, depending on the size of
the sampling site. All fish captured will be identified to species, measured, and released alive
near the point of capture. As per ADF&G Fish Resource Permit stipulations, all salmon eggs
used as bait will be commercially sterilized or disinfected with a 10-minute soak in a 1/100
Betadyne solution prior to use.
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9.5.4.4.6 Snorkel Surveys
This survey technique is most commonly used for juvenile salmonid populations, but can also be
used to assess other species groups. Generally, snorkeling works well for detecting presence or
absence of most species. Limits occur when water is turbid or deep due to the inability to see the
fish, or the water is too swift to safely survey (Dolloff et al. 1993, 1996). To get relative
abundance estimates, a closed population is needed within a single habitat unit, and block nets
will be used to prevent fish from leaving the unit (Hillman et al. 1992).
In stream channels with a width of less than 4 m, the survey will be conducted by a single
snorkeler viewing and counting fish on both sides of the channel, alternating from left to right
counts. In stream channels with a width greater than 4 m, the surveys will be conducted by two
snorkelers working side by side and moving upstream in tandem, with each individual counting
fish on one side of the channel. The counts from all snorkelers are then summed for the total
count for the reach sampled. This expansion estimate assumes that counts are accurate and that
snorkelers are not counting the same fish twice (Thurow 1994). Data will be recorded following
completion of the survey. Survey reaches will be snorkeled starting at the downstream end and
working upstream.
Snorkel surveys will also be used in combination with other techniques to estimate relative
abundance. This use of snorkel surveys provides a calibration factor for the counting efficiency
of snorkel surveys compared to other methods such as electrofishing and seining (Dolloff et al.
1996).
For most of the snorkel surveys in this study, two experienced biologists will snorkel along
standardized transects in clear water areas during both day and night during each field survey
effort. Snorkelers will visually identify and record the number of observed fish by size and
species. The location of each snorkel survey transect will be mapped using hand-held GPS units
and marked on high-resolution aerial photographs.
9.5.4.4.7 Fyke/Hoop Nets
Fyke or hoop nets will be deployed to collect fish in sloughs and side channels with moderate
water velocity (< 3 feet per second). After a satisfactory location has been identified at each site,
the same location will be used during each subsequent collection period. The nets will be
operated continuously for up to two days. Each fyke net will be configured with two wings to
guide the majority of water and fish to the net mouth. The fyke nets will have 1/8-inch mesh, 1-
foot diameter hoops, and up to 4 hoops. Where possible, the guide nets will be configured to
maintain a narrow open channel along one bank. Where the channel size or configuration does
not allow an open channel to be maintained, the area below the fyke net will be checked
regularly to assess whether fish are blocked and cannot pass upstream. A live car will be located
at the downstream end of the fyke net throat to hold captured fish until they can be processed.
The fyke net wings and live car will be checked daily to clear debris and to ensure that captured
fish do not become injured. The location of the fyke net sets will be mapped using a hand-held
GPS unit and marked on high-resolution aerial photographs.
9.5.4.4.8 Hoop Traps
Commercially available hoop traps have been used successfully by ADF&G on the Tanana River
as a non-lethal method to capture burbot for tagging studies (Evenson 1993; Stuby and Evenson
1998). Two sizes of traps have been used. Small and large hoop traps are 3.05 meters (m) and
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3.66 m long, respectively. The small hoop trap has seven 6.35-mm steel hoops with diameters
tapered from 0.61 m at the entrance to 0.46 m at the cod end. The large trap has inside diameters
tapering from 91 to 69 centimeters (cm) with throat diameters of 36 cm. Each trap has a double
throat that narrows to an opening 10 cm in diameter. All netting is knotted nylon woven into 25-
mm bar mesh. Each trap is kept stretched open with two sections of PVC pipe spreader bars
attached by snap clips to the end hoops. Bernard et al. (1991) provides an account of the efficacy
of the small and large traps.
Hoop traps will be deployed in mainstem areas of lower velocity to capture burbot from late
August through early October for radio-tagging (Objectives 1 and 2). Soak times will generally
be overnight, but not more than 12 hours (M. Evenson pers comm 2012). All burbot captured
will be measured and released. Up to 10 radio tags will be surgically implanted in burbot
spatially distributed throughout the Upper Susitna River.
9.5.4.4.9 Beach Seine
Beach seines are an effective method to capture fish in a wide variety of habitats and are most
effective in shallow water areas free of large woody debris and snags such as boulders. Seining
allows the sampling of relatively large areas in short periods of time as well as the capture and
release of fish without significant stress or harm. Repetitive seining over time with standardized
net sizes and standardized deployment in relatively similar habitat can be an effective way to
quantify the relative abundance of certain species over time and space, especially for small
juvenile migrating salmon (Hayes et al. 1996). Beach seines will be 5 feet in depth and 40 feet
in length, 1/4-inch mesh (net body) with a 1/8-inch net bag; however, the actual length of seine
used will depend on the site conditions. Low water conditions may be sampled using a shorter
and shallower beach seine; as long as the area sampled is noted and the net is deep enough to fill
the water column, then comparisons can be made. The location fished will be mapped using
hand-held GPS units and marked on high-resolution aerial photographs. The area swept will be
noted. Repetitive seining over time with standardized nets and soak times in relatively similar
habitats can be an effective way to quantify the relative abundance of certain species over time
and space, especially for small juvenile migrating salmon. To the extent possible, the same area
will be fished during each sampling event; net sizes and soak times will be standardized.
9.5.4.4.10 Out-Migrant Trap
Rotary screw traps are useful for determining the timing of emigration by downstream migrating
juvenile salmonids and resident fish (Objective 2). Out-migrant traps will be installed in a
maximum of two sites: one site located near the proposed Watana Dam and one site near a
tributary mouth. The location will occur with input from the Fish and Aquatic TWG and will be
based on the physical conditions at the selected sites and logistics for deploying, retrieving, and
maintaining the traps. Flow conditions permitting, traps will be fished on a cycle of 48 hours on,
72 hours off throughout the ice-free period. Each trap will be checked at least twice per day.
9.5.4.4.11 Fish Handling
Field crews will record the date, start and stop times, and level of effort for all sampling events,
as well as water temperature and dissolved oxygen at sampling locations. All captured fish will
be identified to species. Up to 100 individuals per species per life stage per season will be
measured to the nearest mm fork length, and in Focus Areas up to 30 fish per species per site will
be measured on a monthly basis. Sampling supplies will be prepared before sampling begins.
For example, the date, location, habitat type, and gear type recorded in log book, beginning fish
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number in proper sequence, daily sample objective by gear type, and an adequate live box and
clean area should be available. To increase efficiency, fish should be sampled in order in groups
of 10, and the sample routine followed in a stepwise manner: (1) identify species and life stage,
(2) measure lengths, (3) remove tissue samples for genetic analysis, and (4) cut all dead fish for
accurate sex identification. Care will be taken to collect all data with a consistent routine and to
record data neatly and legibly.
For methods in which fish are observed, but not captured (i.e., snorkeling, DIDSON, and
underwater video), an attempt will be made to identify all fish to species. For snorkeling, fork
length of fish observed will be estimated within 40-mm bin sizes. If present, observations of
poor fish condition, lesions, external tumors, or other abnormalities will be noted. When more
than 30 fish of a similar size class and species are collected at one time, the total number will be
recorded and a subset of the sample will be measured to describe size classes for each species.
All juvenile salmon, rainbow trout, Arctic grayling, Dolly Varden, burbot, and whitefish greater
than 60 mm in length will be scanned for PIT tags using a portable tag reader. A PIT tag will be
implanted into a sub-sample of fish of these species that do not have tags and are approximately
60 mm and larger. Because Chinook salmon are of particular interest and in low abundance, all
captured juvenile Chinook salmon of taggable size will receive tags. For selected species, up to
1,000 fish per species per PIT tag array will be tagged based on proximity to PIT arrays. Target
species are Dolly Varden, humpback whitefish, round whitefish, northern pike, Arctic grayling,
and burbot. Radio transmitters will be surgically implanted in up to 30 adult fish of sufficient
body size of each species and distributed temporally and longitudinally in the Upper River.
In support of the bioenergetics modeling (Objective 5, Section 9.8.4.5.1), fish species targeted
for dietary analysis will include juvenile Chinook and coho salmon, juvenile and adult rainbow
trout. Of these species Chinook salmon and rainbow trout may be encountered in the Upper
River. A total of five fish per species/age class per sampling site collection will be sampled for
fish stomach contents, using non-lethal methods (described in Section 9.8.4.7). All fish will
have fork length and weight recorded with the stomach sample. In addition, scales will be
collected from the preferred area of the fish, below and posterior to the dorsal fin, for age and
growth analysis. At two selected sample collection locations (one each in Upper and Middle
River), punch samples of muscle tissue will be obtained from each fish for use in the stable
isotope analysis (Section 9.8.4.5.2).
Otoliths will be collected from Dolly Varden and humpback whitefish greater than 200 mm (7.8
inches) in length to test for marine-derived elements indicative of an anadromous life history
pattern (Objective 4). It is assumed that larger fish are more likely to have exhibited anadromy
and therefore it is proposed to collect otoliths only from fish greater than 200 mm. A target of 30
fish of each species during 2013 and 2014 will be collected (60 fish of each species total).
Tissue, fillets, and/or liver (burbot only) samples will also be collected in the mainstem Susitna
River for assessment of metals concentrations (Objective 5) (see Section 5.5.4.7 Water Quality
and Section 5.7.4.2.6, Mercury Assessment and Potential for Bioaccumulation Study). Target
fish species in the vicinity of the Watana Reservoir will be Dolly Varden, Arctic grayling,
stickleback, whitefish species, burbot, longnose sucker, and resident rainbow trout. If possible,
fillets will be sampled from seven adult individuals from each species. Larger, older fish tend to
have higher mercury concentrations; these fish will therefore be targeted with a desired sample
size of seven per species. Body size targeted for collection will represent the non-anadromous
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phase of each species’ life cycle. For stickleback, whole fish samples will need to be used.
Collection times for fish samples will occur in late August and early September.
Tissue samples will be collected opportunistically in conjunction with all fish capture methods
from selected resident and non-salmon fish to support the Genetic Baseline Study (Objective 7;
Section 9.14). Tissue samples will include an axillary process from all adult salmon, caudal fin
clips from fish >60 mm, and whole fish <60 mm. The target number of samples, species of
interest, and protocols are outlined in Section 9.14.
9.5.4.4.12 Remote Fish Telemetry
Remote telemetry techniques will include radio telemetry and PIT tags. Both of these methods
are intended to provide detailed information from relatively few individual fish. PIT tags will be
surgically implanted in small fish >60 mm; radio transmitters will be surgically implanted in
adult fish of sufficient body size of selected species distributed temporally and longitudinally in
the Upper River. The target species to radio-tag include Dolly Varden, humpback whitefish,
round whitefish, northern pike, Arctic grayling, and burbot. Radio-tracking provides information
on fine and large spatial scales related to location, speed of movement, and habitat utilization by
surveying large areas and relocating tagged individuals during aerial, boat, and foot surveys. PIT
tags can be used to document relatively localized movements of fish as well as growth
information from tagged individuals across seasons and years. However, the “re-sighting” of
PIT-tagged fish is limited to the sites where antenna arrays are placed. To determine movement
in and out of side sloughs or tributaries requires that tagged fish pass within several feet of an
antenna array, thereby limiting its use to sufficiently small water bodies. To characterize growth
rates, fish must be recaptured, checked for a tag, and measured.
Radio Telemetry
The primary function of the telemetry component is to track tagged fish spatially and temporally
with a combination of fixed station receivers and mobile tracking. Time/date stamped, coded
radio signals from tags implanted in fish will be recorded by fixed station or mobile positioning.
All telemetry gear (tags and receivers) across both studies will be provided by ATS, Inc.
(Advanced Telemetry Systems, www.atstrack.com).
The types of behavior to be characterized include the following:
Arrival and departure timing at specific locations/positions
Direction of travel
Residence time at specific locations/positions
Travel time between locations/positions
Identification of migratory, holding, and spawning time and locations/positions
Movement patterns in and between habitats in relation to water conditions (e.g.,
discharge, temperature, turbidity)
Locating radio-tagged fish will be achieved by fixed receiver stations and mobile surveys (aerial,
boat, and foot). Fixed stations will largely be those used for the Salmon Escapement Study
(Section 9.7), of which, only one is slated for installation in the Upper River at the Kosina Creek
confluence (RM 206.8). Up to three additional fixed stations may be established at strategic
locations with input from the Fish and Aquatic TWG. These stations will be serviced in
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conjunction with the Salmon Escapement Study during the July through October period, but will
be extended to begin on June 1 to track resident fish. Fixed stations will be downloaded as
power supplies necessitate and up to twice monthly during the salmon spawning period
(approximately July through October). The Salmon Escapement Study will provide
approximately weekly aerial survey coverage of the study area (approximately July through
October). At other times of the year, the frequency of aerial surveys will be monthly and during
critical species-specific time periods (e.g., burbot spawning), bi-weekly. Using the guidance of
fixed-station and aerial survey data on the known positions of tagged fish, specific locations of
any concentrations of tagged fish that are suspected to be spawning will be visited to obtain
individual fish positions. Foot and boat surveys will be conducted approximately July through
October as part of the Salmon Escapement Study (Section 9.7). Spatial and temporal allocation
of survey effort will be finalized based on the actual locations and number of each species of fish
tagged.
The fundamental reason for using radio telemetry as a method to characterize resident and non-
salmonid anadromous species is that it can provide useful information to address the overarching
goal of the study and several of its objectives. In particular, radio telemetry can provide data on
seasonal distribution and movement of the target fish throughout the range of potential habitats.
Relocation data from the radio telemetry component of this study will be used to characterize the
timing of use and degree of movements among macrohabitats and over periods during which the
radio-tags remain active (potentially two or three seasons for large fish). This objective may be
achieved by the use of long-life tags (e.g., greater than one year) and shorter life tags (e.g., three-
month tags) applied to appropriate-sized fish over time. In general, successful radio telemetry
studies use a tag weight to fish weight guideline of 3 percent (with a common range of 2 to 5
percent depending on the species). The range in size encountered for a particular species may be
broad enough to warrant the use of different-sized tags with different operational life
specifications. Actual tag life will be determined by the appropriate tag for the size of the fish
available for tagging.
In this regard, the range in weights for the seven target species to be radio-tagged was estimated.
Fish weights and the respective target weight of radio-tags (Table 9.5-3) were calculated using
existing or derived length–weight relationships for Alaska fish (Figure 9.5-3), and length
frequency distributions for Susitna River fish. This analysis illustrates that there is a relatively
broad range of potential tag weights (0.5 grams [g] to 81 g) that are necessary to tag each species
over the potential range in fish size. Further, it is evident that some species will require tags with
a relatively short (30 to 200 days) operational period (tag life).
The broad range in tag weight complicates the scope of the task in terms of technological
feasibility. In general, there is a preference for using coded tags because it allows the unique
identification of a hundred tags on a single frequency. Conversely, standard tags (not coded)
require a single frequency for each tagged fish to allow unique identification. The radio
telemetry industry provides a variety of equipment to match research needs, but there are always
trade-offs in terms of tracking performance and cost between different systems. This plan
intends to capitalize on the use of the existing telemetry platform (ATS telemetry equipment) to
sufficiently monitor the target species, but directly constrains the potential options for tagging
and monitoring. More specifically, the smallest ATS coded tag weighs 6 g and therefore
precludes application to all the species at the lower portion of their most frequently occurring
size range (Table 9.5-3). For example, if fish need to weigh a minimum of 200 g to be tagged,
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then Dolly Varden would be tagged only at its largest samples, and burbot would be tagged
almost across its entire adult size range (Table 9.5-3) based on their respective length–frequency
distributions.
The use of non-coded tags on the smaller adult fish would require the use of many frequencies
(e.g., 50 to 150) and an entirely separate array of receivers. Overall, tagging fish weighing less
than 200 g would be expensive and logistically inefficient. The only viable option to cover the
entire range of fish sizes would be to use alternative vendors’ radio telemetry receivers and tags
that use coded technology through the entire range of tag sizes (e.g., Lotek Wireless).
Tags will be surgically implanted in up to 30 fish of sufficient body size of each species
distributed temporally and longitudinally in the Upper River. These fish will be captured during
sampling events targeting adult fish and with directed effort using a variety of methods. The
final spatial and temporal allocation of tags will be determined after 2012 study results are
available (i.e., preliminary fish abundance and distribution). The tag’s signal pulse duration and
frequency, and, where appropriate, the transmit duty cycle, will be a function of the life history
of the fish and configured to maximize battery life and optimize the data collection. Larger tags
can accommodate the greatest battery life and therefore will be used when fish are large enough,
but smaller, shorter life tags will be used across the range of adult body sizes.
PIT Tag Antenna Arrays
As described above, fish of appropriate size from target species will be implanted with a PIT
tagged for mark-recapture studies. Half-duplex PIT tags either 12 mm in length or 23 mm in
length will be used, depending on the size of the fish to be implanted. Each PIT tag has a unique
code that allows identification of individuals. Recaptured fish will provide information on the
distance and time travelled since the fish was last handled and changes in fish length and weight.
PIT tag antenna arrays with automated data logging will be deployed at up to six selected side
channel, slough, and tributary mouths to detect movement of tagged fish into or out of the site
with particular focus on juvenile Chinook salmon. With input from the Fish and Aquatic TWG,
site selection for antenna arrays will be based on habitats and tributaries identified as suitable
habitat for juvenile Chinook salmon. A variety of antenna types may be used including hoop
antennas, swim-over antennas, single rectangle (swim-through) antennas, or multiplexed
rectangle antennas to determine the directionality of movement. Antennas will be deployed
shortly after ice-out in 2013. Data loggers will be downloaded every two to four weeks
depending on the need to replace batteries and on reliability of logging systems. Power to the
antennas will be supplemented with solar panels.
All juvenile Chinook salmon 60 mm or greater in length will be PIT-tagged. For selected
species, up to 1,000 fish per species per PIT tag array will be tagged based on proximity to PIT
arrays. Target species are Dolly Varden, humpback whitefish, round whitefish, northern pike,
Arctic grayling, and burbot.
9.5.4.4.13 DIDSON and Video Cameras
DIDSON and video cameras are proposed to survey selected sloughs and side channels. The
deployment techniques will follow those described by Mueller et al. (2006). Mueller et al.
(2006) found that DIDSON cameras were useful for counting and measuring fish up to 52.5 feet
(16 meters) from the camera and were effective in turbid waters. In contrast, they found that
video cameras were only effective in clear water areas with turbidity of less than four
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nephelometric turbidity units (NTU). However, Mueller et al. (2006) noted that identifying
species and observing habitat conditions were more effective with video cameras than DIDSON
cameras.
DIDSON is a high-resolution imaging sonar that provides video-type images over a 29-degree
field of view and can thus be used to observe fish behavior associated with spawning, i.e.,
dynamic behavior that cannot be identified on the static side-scan sonar images. To obtain high-
quality images of adult salmon, the maximum range will be limited to 15 meters (49 feet).
Within this field of view, evidence of spawning behavior, e.g., redd digging, chasing, spawning,
will be clearly identifiable. Furthermore, on DIDSON images fish can be classified by size
category, e.g., <40 centimeters, 40 – 70 centimeters, >70 centimeters (<5 inches, 25-44 inches,
>44 inches, respectively). Although this is not sufficient for definitive species identification, it
will allow recognition of smaller resident fish, medium-sized adult salmon, and large Chinook
salmon.
Underwater video imaging can record images in real-time over short time intervals and can
provide information on fish species presence/absence in the immediate vicinity. Video systems
can also be configured to record images for longer periods of time using time lapse or motion
triggered recorders. Although water clarity and lighting can limit the effectiveness of video
sampling, a distinct advantage of video over DIDSON is the ability to clearly identify fish
species. In clear water under optimal lighting, video can capture a much larger coverage area
than DIDSON (Mueller et al. 2006). Video is often combined with a white or infrared (IR) light
source especially under ice and in low light northern latitudes; however, lighting may affect fish
behavior. Since nighttime surveys will be required to identify possible diurnal changes in fish
behavior and habitat use, the video system will be fitted with IR light in the form of light
emitting diodes that will surround the lens of the camera. Muller et al. (2006) reported that most
fish are unaffected by IR lights operated at longer wavelengths because it falls beyond their
spectral range. In addition, the video system will be equipped with a digital video recorder for
reviewing and archiving footage of fish observations.
9.5.5. Consistency with Generally Accepted Scientific Practices
This study plan was developed by fisheries scientists in collaboration with the Fish and Aquatic
TWG and draws upon a variety of methods including many that have been published in peer-
reviewed scientific journals. As such, the methods chosen to accomplish this effort are consistent
with standard techniques used throughout the fisheries scientific community. However,
logistical and safety constraints inherent in fish sampling in a large river in northern latitudes
also play a role in selecting appropriate methodologies. In addition, some survey methods may
not be used in the mainstem river immediately upstream of Devils Canyon to avoid any risk of
being swept into the canyon. During the 1980s studies, no surveys were conducted on the
mainstem river from RM 150 to RM 189.0, except for spawning surveys conducted by
helicopter.
9.5.6. Schedule
Initial data collection efforts for this multi-year study began in the summer/fall of 2012 and will
commence after the FERC study plan determination in early 2013 and continue through October
2014. The schedule allows for two complete open water study seasons. The proposed schedule
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(Table 9.5-4) for completion of the Study of Fish Distribution and Abundance in the Upper
Susitna River is as follows:
Initial collection efforts (Chinook salmon spawning surveys and fish trapping targeting
juvenile Chinook salmon) in Upper River tributary streams – July to October 2012
File a supplemental memorandum with the FERC reporting interim 2012 collection
results – First quarter 2013
Development of Implementation Plan and selection of study sites – January to March
2013
Open water fieldwork – May to October 2013 and May to October 2014
Reporting of interim results – September 2013 and 2014
Quality control check of geospatially-referenced relational database – December 2013
and 2014
Data analysis – October to December 2013 and October to December 2014
Initial and Revised Study Reports on 2013 and 2014 activities – anticipated to be filed
during the first quarter of 2014 and 2015, one and two years, respectively, after the FERC
Study Plan Determination (February 2013)
9.5.7. Relationship with Other Studies
Over the study implementation phase, an iterative process of information exchange will take
place between interrelated studies that depend upon one another for specimen collection or data.
As studies collect and synthesize data, findings will be disseminated to interdependent studies.
In addition to providing baseline information about aquatic resources in the Project area, aspects
of this study are designed to complement and support other fish and aquatic studies (Figure 9.5-
4). Fish collections in the Upper River will identify species that could colonize the future
reservoir site (Section 9.10) and help validate fish periodicity, habitat associations, and selection
of target species for reach-specific analyses for the Fish and Aquatics Instream Flow Study
(Section 8.5). Patterns of distribution and abundance from traditional sampling methods will
help validate and complement information from radio telemetry, fishwheel, and sonar
observations of salmon in the Salmon Escapement Study (Section 9.7). The Salmon Escapement
Study will provide fixed receiver and aerial tracking of fish radio-tagged in this study. Fish
movement, habitat association, and growth data will provide inputs for bioenergetics and trophic
analysis modeling for the River Productivity Study (Section 9.8). Additionally, targeted species
will be sampled for fish stomach contents in support of the bioenergetics modeling component.
Fish distribution and abundance will complement information about harvest rates and effort
expended by commercial, sport, and subsistence fisheries to support the Fish Harvest Study
(Section 9.15). Fish collections and observations in conjunction with aquatic habitat
characterization will aid in the development of fish and habitat associations for the
Characterization and Mapping of Aquatic Habitats Study (Section 9.9). Fish collections will
provide data on fish use in sloughs and tributaries with seasonal flow-related or permanent fish
barriers for the Study of Fish Passage Barriers in the Middle and Upper Susitna River and
Susitna Tributaries (Section 9.12) and will provide information for the Study of Fish Passage
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Feasibility at Watana Dam (Section 9.11). Fish tissue sample collections will support the
Genetics Baseline Study for Selected Fish Species (Section 9.14) and the Mercury Assessment
and Potential for Bioaccumulation Study (Section 5.7).
9.5.8. Level of Effort and Cost
Initial data collection efforts for this multi-year study began in the summer/fall 2012 and will
commence after the FERC study plan determination in early 2013 and continue until March
2015. Sampling will be conducted according to a stratified scheme designed to cover a range of
habitat types with a minimum of three replicates each. The level of effort at each sample site and
sampling frequency will vary based on tasks and objectives. Selection of sampling sites will be
influenced by the results of the Characterization and Mapping of Aquatic Habitats Study
(Section 9.9) and tributary habitat mapping and fish sampling conducted by AEA during 2012,
which may indicate that some tributaries are unsuitable for sampling because of safety issues or
passage barriers.
The number and size of sample sites and sampling frequency require a large-scale field effort
and subsequent data compilation, as well as quality assurance/quality control (QA/QC) and
analysis efforts. Generally:
Sampling will be conducted seasonally during the ice-free period in all study sites.
Sampling will be conducted more frequently immediately following break-up to
document seasonal movement patterns of juvenile Chinook salmon from natal tributaries
to rearing habitats.
Fish capture and observation methods may include snorkeling, seining, gillnetting,
minnow trapping, angling, trot lines, and out-migrant traps depending on stream
conditions such as depth, flow, and turbidity, target species, and life stage.
Field crews will consist of two to four individuals, depending on sampling method used.
Sampling in remote areas requires helicopter, fixed-wing airplane, and boat support.
Radio-tracking of tagged fish includes 12 aerial surveys, and foot and boat surveys as
necessary.
The estimated cost for implementing the Study of Fish Distribution and Abundance in the Upper
Susitna River is $2,500,000.
9.5.9. Literature Cited
ADF&G (Alaska Department of Fish and Game). 1982. Aquatic Studies Procedures Manual:
Phase I. Su-Hydro Aquatic Studies Program. Anchorage, Alaska. 111 pp.
ADF&G. 1983. Aquatic Studies Procedures Manual: Phase II - Final Draft 1982-1983. Alaska
Department of Fish and Game. Su-Hydro Aquatic Studies Program. Anchorage, Alaska.
257 pp.
ADF&G. 1984. ADF&G Su Hydro Aquatic Studies May 1983 - June 1984 Procedures Manual
Final Draft. Alaska Department of Fish and Game. Su-Hydro Aquatic Studies Program.
Anchorage, Alaska.
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ADF&G. 1985. Adult salmon investigations, May-October 1984. ADF&G Susitna Hydro
Aquatic Studies Report No. 6 Susitna Hydro Document No. 2748. Anchorage, Alaska.
AEA (Alaska Energy Authority). 2011a. Pre-application Document (PAD): Susitna-Watana
Hydroelectric Project FERC Project No. 14241. December 2011. Prepared for the Federal
Energy Regulatory Commission, Washington, D.C.
AEA. 2011b. Aquatic Resources Gap Analysis. Prepared by HDR, Inc., Anchorage. 107
pp.Barrett, B. M. 1985. Adult Salmon Investigations, May - October 1984. Alaska
Department of Fish and Game, Susitna Hydro Aquatic Studies, Anchorage, Alaska. 528
pp.
Barrett, B. M., F. M. Thompson, S. Wick, and S. Krueger. 1983. Adult Anadromous Fish
Studies, 1982. Alaska Department of Fish and Game, Susitna Hydro Aquatic Studies,
Anchorage, Alaska. 275 pp.
Bernard, D. R., G. A. Pearse, and R. H. Conrad. 1991. Hoop traps as a means to capture burbot.
North American Journal of Fisheries Management 11:91-104.
Bryant, M. D. 2000. Estimating Fish Populations by Removal Methods with Minnow Traps in
Southeast Alaska Streams. North American Journal of Fisheries Management 20:923-
930, 2000.
Buckwalter, J.D. 2011. Synopsis of ADF&G's Upper Susitna Drainage Fish Inventory, August
2011. Alaska Department of Fish and Game, Division of Sport Fish, Anchorage, Alaska.
27 pp.
Delaney, K., D. Crawford, L. Dugan, S. Hale, K. Kuntz, B. Marshall, J. Mauney, J. Quinn, K.
Roth, P. Suchanek, R. Sundet, and M. Stratton. 1981a. Resident Fish Investigation on
the Upper Susitna River. Alaska Department of Fish and Game, Anchorage, AK. 157
pp.
Dolloff, C.A., D.G. Hankin, G.H Reeves. 1993. Basinwide estimation of habitat and fish
populations in streams. USDA Forest Service General Technical Report SE-GTR-83. 25
p.
Dolloff, A., J. Kershner, R. Thurow. 1996. Underwater Observation. Pp. 533-554 In Fisheries
Techniques, Murphy and Willis (eds), American Fisheries Society, Bethesda Maryland,
732 p.
Evenson, M. J. 1993. Seasonal movements of radio-implanted burbot in the Tanana River
Drainage. Alaska Department of Fish and Game Fishery Data Series No. 93-47,
Fairbanks, AK. 35 pp.
Hayes, D. B., C. P. Ferreri, and W. W. Taylor. 1996. Active fish capture methods. Pages 193–
220 In B. R. Murphy and D. W. Willis, editors. Fisheries techniques. American Fisheries
Society, Bethesda, Maryland.
Hillman, T. W., J. W. Mullan, J. S. Griffith. 1992. Accuracy of underwater counts of juvenile
chinook salmon, coho salmon, and steelhead. North American Journal of Fisheries
Management. 12:598-603.
Mueller, R.P., R.S. Brown, H. Hop, and L. Moulton. 2006. Video and acoustic camera
techniques for studying fish under ice: a review and comparison. (16):213-226. Nemeth,
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M.J., A. M. Baker, B. C. Williams, S. W. Raborn, J. T. Priest, and S. T. Crawford. 2010.
Movement and abundance of freshwater fish in the Chuit River, Alaska, May through
July, 2009. Annual report prepared by LGL Alaska Research Associates, Inc.,
Anchorage, Alaska for PacRim Coal, L.P. 86 pp.
NMFS. 2000. Guidelines for electrofishing waters containing salmonids listed under the
Endangered Species Act. 5 pp.
Rutz, D.S. 1999. Movements, food availability and stomach contents of Northern Pike in
selected Susitna River drainages, 1996-1997. Alaska Department of Fish and Game
Fishery Data Series No. 99-5. Anchorage, Alaska. 78 pp.
Sautner, J., and M. Stratton. 1983. Upper Susitna River Impoundment Studies 1982. Alaska
Department of Fish and Game. Anchorage, Alaska. 220 pp.
Schmidt, D.C., S.S. Hale, and D.L. Crawford. 1985. Resident and juvenile anadromous fish
investigations (May - October 1984). Alaska Department of Fish and Game, Anchorage,
Alaska. 483 pp.
Stuby, L. and M. J. Evenson. 1998. Burbot research in rivers of the Tanana River Drainage,
1998. Alaska Department of Fish and Game Fishery Data Series No. 99-36, Fairbanks,
AK. 66 pp.
Thompson, F. M., S. Wick, and B. Stratton. 1986. Report No 13, Volume I, Adult Salmon
Investigations: May - October 1985. Alaska Department of Fish and Game, APA
Document No 3412, Anchorage, Alaska. 173 pp.
Thurow, R.F. 1994. Underwater methods for study of salmonids in the Intermountain West. U.S.
Dept of Agriculture, Forest Service, Intermountain Research Station. General Technical
Report INT-GTR-307. Odgen, Utah. 28 p.
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9.5.10. Tables
Table 9.5-1. Summary of life history, known Susitna River usage of fish species within the Upper Susitna River
Segment (compiled from Delaney et al. 1981).
Common Name Scientific Name Life Historya Susitna Usageb Distributionc
Arctic grayling Thymallus arcticus F O, R, P Low, Mid, Up
Burbot Lota lota F O, R, P Low, Mid, Up
Chinook salmon Oncorhynchus tshawytscha A M2, R Low, Mid, Up
Dolly Varden Salvelinus malma A,F O, P Low, Mid, Up
Humpback whitefishd Coregonus pidschian A,F O, R, P Low, Mid, Up
Lake trout Salvelinus namaycush F U U
Longnose sucker Catostomus catostomus F R, P Low, Mid, Up
Round whitefish Prosopium cylindraceum F O, M2, P Low, Mid, Up
Sculpine Cottid M1, F P Low, Mid, Up
a A = anadromous, F = freshwater, M1 = marine
b O = overwintering, P = present, R = rearing, S = spawning, U = unknown, M2 = migration
c Low = Lower River, Mid = Middle River, Up = Upper River, U = unknown
d Whitefish species that were not identifiable to species by physical characteristics in the field were called humpback by
default. This group may have contained Lake (Coregonus clupeaformis), or Alaska (Coregonus nelsonii) whitefish.
e Sculpin species generally were not differentiated in the field. This group may have included Slimy (Cottus cognatus),
Prickly (Cottus asper), Coastal range (Cottus aleuticus), and Pacific staghorn (Leptocottus armatus).
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REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-30 December 2012 Table 9.5-2. Proposed methods by objective, task, species, and life stage. Obj Task Species/ Life stage Study Sites Proposed Methods by Season 1A Distribution Juvenile salmon, non-salmon anadromous, resident Representative habitat types Single pass sampling Selection of methods will be site-specific, species-specific, and life-stage-specific. For juvenile and small fish sampling, electrofishing, snorkeling, seining, fyke nets, angling, DIDSON and video camera where feasible and appropriate. For adults, directed efforts with seines, gillnets, trot lines, and angling. To the extent possible, the selected transects will be standardized and the methods will be repeated during each sampling period at a specific site to evaluate temporal changes in fish distribution. Additional info from radio telemetry studies (Objective #2). 1B Relative abundance Juvenile salmon, non-salmon anadromous, resident Representative habitat types Multi-pass sampling To the extent possible, the selected transects will be standardized and the methods will be repeated during each sampling period at a specific site to evaluate temporal changes in fish distribution. Snorkeling, beach seine, electrofishing, fyke nets, gillnet, minnow traps, fishwheels, out-migrant traps, etc. 1C Fish habitat associations Juvenile salmon, non-salmon anadromous, resident Representative habitat types Analysis of data collected under Objective 1: Distribution. Combination of fish presence, distribution, and density by mesohabitat type by season. 2A Timing of downstream movement and catch using out-migrant traps All species; juveniles At selected out-migrant trap & PIT tag array sites Out-migrant Traps: Maximum of 2. One near the proposed dam site; one near the mouth of a known Chinook salmon spawning tributary. Combine with fyke net sampling to identify key site-specific differences. Sampling in mainstem off-channel habitats downstream of tributaries with fyke nets, seines, and out-migrant traps 2B Describe seasonal movements using biotelemetry (PIT and radio-tags) All species PIT arrays sites River-wide aerial tracking surveys PIT tags: tags opportunistically implanted from a variety of capture methods in Focus Areas. Antenna arrays in up to 6 sites at selected side channel, side slough, tributary mouth, and upland sloughs in the Upper River. Radio-tags surgically implanted in up to 30 fish of sufficient body size of each species distributed temporally & longitudinally. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-31 December 2012 Obj Task Species/ Life stage Study Sites Proposed Methods by Season 2C Describe juvenile Chinook salmon movements Juvenile Chinook salmon Representative habitat types PIT tag arrays at tributary mouths, sloughs, and side channels (Obj 2B) Outmigrant trap in known Chinook spawning tributary DIDSON or underwater video to monitor movement into or out of specific habitats Monthly measurements of fish size/ growth 5 Document age structure, growth, and condition by season Juvenile anadromous and resident fish All study sites for Obj 1B Stock biology measurements – length from captured fish up to 100 individuals per season per species per life stage . Emphasis placed on juvenile Chinook salmon. 6 Seasonal presence/absence and habitat associations of invasive species Northern pike All study sites Same methods as #1 and #2 above. The presence/absence of northern pike and other invasive fish species will be documented in all samples Additional direct efforts with angling as necessary 7 Collect tissue samples to support the Genetic Baseline Study All All study sites in which fish are handled Opportunistic collections in conjunction with all capture methods listed above. Tissue samples include axillary process from all adult salmon, caudal fin clips from fish >60 mm, and whole fish <60 mm. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
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Table 9.5-3. Length and weight of fish species to be radio-tagged and respective target radio-tag weights.
All sizes Most likely to be caught
Species
Length
(mm) Weight (g)
Fish
Length
(mm)
Est.
Weight
Min (g)
Est.
Weight
Max (g)
Tag
Weight
of Min
(3%)
Tag
Weight
of Max
(3%)
Fish length
(mm) @ 200 g
weight
Arctic grayling 36–444 <1–830 120–420 18 705 0.5 21.2 270
Dolly Varden 30–470 <1–1,007 130–300 20 256 0.6 7.7 277
Round whitefish 23–469 <1–1,035 150–390 23 553 0.7 16.6 287
Rainbow trout 27–612 <1–3,327 180–480 96 1635 2.9 49.1 232
Humpback whitefish 30–510 <1–1,544 210–450 180 1141 5.4 34.2 219
Burbot 26–791 <1–3,532 300–510 186 931 5.6 27.9 307
Northern pike 83–713 5–2707 200-700 62 2700 1.9 81.0 296
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Table 9.5–4. Schedule for implementation of the Fish Distribution and Abundance in the Upper Susitna River.
Activity
2012 2013 2014 2015
1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q
Initial Studies and Technical Memo
Study Site Selection
Develop and File Implementation Plan
Fish Sampling --------
Data Entry
Preliminary Data Analysis
Initial Study Report Δ
Final Data Analysis
Updated Study Report ▲
Legend:
Planned Activity
----- Follow-up activity (as needed)
Technical Memorandum
Implementation Plan
Δ Initial Study Report
▲ Updated Study Report
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REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-35 December 2012 Figure 9.5-2. Schematic showing strata by habitat type for relative abundance sampling for the Upper River. Note that level two stratification within geomorphic reach, is not depicted in this figure because not all habitat types will be present within each geomorphic reach in the Upper River. The selection of habitats to sample will be distributed across geomorphic reaches as described in the Upper Susitna River Fish Distribution and Abundance Implementation Plan and in Section 9.5.4.1. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
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Figure 9.5–3. Existing or derived length–weight relationships for fish species to be radio-tagged.
0
200
400
600
800
1000
1200
1400
1600
1800
2000
0 100 200 300 400 500 600Weight (g)Length (mm)
RBTR DLVD
PIKE BRBT
RDWF HBWF
GRAY
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9.6. Study of Fish Distribution and Abundance in the Middle and
Lower Susitna River
9.6.1. General Description of the Proposed Study
This study is focused on describing the current fish assemblage including spatial and temporal
distribution, and relative abundance by species and life stage in the Susitna River downstream of
the proposed Watana Dam (river mile [RM] 184) with emphasis on early life history of
salmonids and seasonal movements of selected species. Fishery resources in the Susitna River
basin consist of a variety of salmonid and non-salmonid resident fish (Table 9.6-1). Adult salmon
species are addressed in the Salmon Escapement Study (Section 9.7).
The physical habitat modeling efforts proposed elsewhere in this RSP require information on the
distribution and periodicity of different life stages for the fish species of interest. Not all life
stages of the target fish species may be present throughout the Middle and Lower Susitna River,
and seasonal differences may occur in their use of some habitats. For example, some fish that
use tributary streams during the open-water period may overwinter in mainstem habitats such as
groundwater-fed sloughs.
This study is designed to provide baseline biological information and supporting information for
the Fish and Aquatics Instream Flow Study (Section 8.5). This study will obtain key life history
information about the fish in Middle and Lower Susitna River using two sampling approaches.
The first sampling approach is focused on gathering data on general fish distribution
(presence/absence); this approach generally involves a single pass with appropriate gear types.
The second sampling approach is to gather data on relative abundance as determined by catch
per unit effort (CPUE) along with complementary data on fish size, age, and condition; this
generally involves multi-pass sampling with standardized transects and gear soak times. The
second approach will also emphasize the identification of foraging, spawning, and overwintering
habitats.
Study Goals and Objectives
Construction and operation of the Project will affect flow, water depth, surface water elevation,
water temperature, and sediment dynamics, among other variables, in the mainstem channel as
well as at tributary confluences, side channels, and sloughs, both in the area of inundation
upstream from the Watana Dam site and downstream in the potential zone of Project hydrologic
influence. These changes can have beneficial or adverse effects upon the aquatic communities
residing in the river. To assess the effects of river regulation on fish populations, an
understanding of existing conditions is needed. Baseline information will be used to predict the
likely extent and nature of potential changes that will occur due to the Project’s effects on
instream flow and water quality.
The overarching goal of this study is to characterize the current distributions, relative
abundances, run timings, and life histories of all resident and non-salmon anadromous species
encountered including, but not limited to Dolly Varden, eulachon, humpback whitefish, round
whitefish, arctic grayling, northern pike, burbot, and Arctic lamprey, as well as freshwater
rearing life stages of anadromous salmonids (fry and juveniles) in the Middle and Lower Susitna
River. Specific objectives include the following:
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1) Describe the seasonal distribution, relative abundance (as determined by CPUE, fish
density, and counts) and fish habitat associations of juvenile anadromous salmonids, non-
salmonid anadromous fishes and resident fishes.
2) Describe seasonal movements of juvenile salmonids and selected fish species such as
rainbow trout, Dolly Varden, humpback whitefish, round whitefish, northern pike, Arctic
lamprey, Arctic grayling, and burbot, with emphasis on identifying foraging, spawning
and overwintering habitats within the mainstem of the Susitna River.
a. Document the timing of downstream movement and catch using out-migrant
traps.
b. Describe seasonal movements using biotelemetry (passive integrated transponder
[PIT] and radio-tags).
3) Describe early life history, timing, and movements of anadromous salmonids.
a. Describe emergence timing of salmonids.
b. Determine movement patterns and timing of juvenile salmonids from spawning to
rearing habitats.
c. Determine juvenile salmonid diurnal behavior by season.
d. Collect baseline data to support the Stranding and Trapping Study.
4) Document winter movements and timing and location of spawning for burbot, humpback
whitefish, and round whitefish.
5) Document the seasonal age class structure, growth, and condition of juvenile anadromous
and resident fish by habitat type.
6) Document the seasonal distribution, relative abundance, and habitat associations of
invasive species (northern pike).
7) Collect tissue samples from juvenile salmon and opportunistically from all resident and
non-salmon anadromous fish to support the Fish Genetic Baseline Study (Section 9.14).
9.6.2. Existing Information and Need for Additional Information
Information regarding resident species, non-salmon anadromous species, and the freshwater
rearing life stages of anadromous salmon was collected as part of the studies conducted during
the early 1980s. Existing information includes the spatial and temporal distribution of fish
species and their relative abundance. The Pre-Application Document (PAD) (AEA 2011a) and
Aquatic Resources Data Gap Analysis (ARDGA; AEA 2011b) summarized this existing
information and also identified data gaps for resident and rearing anadromous fish.
Approximately 18 anadromous and resident fish species have been documented in the Susitna
River drainage (Table 9.6-1). Three additional species are considered likely to be present, but
have not been documented. To varying degrees, the relative abundances and distributions of
these species were determined during the early 1980s studies. For most species, the dominant
age classes and sex ratios were also determined, and movements, spawning habitats, and
overwintering habitats were identified for certain species. Resident species that have been
identified in all three segments of the Susitna River include Arctic grayling, Dolly Varden,
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humpback whitefish, round whitefish, burbot, longnose sucker, and sculpin. Other species that
were observed in the Middle and Lower Susitna River Segments include Bering cisco, threespine
stickleback, arctic lamprey, and rainbow trout. Eulachon have been documented only in the
Lower Susitna River Segment.
Species that have not been documented, but may occur in the Susitna drainage include lake trout,
Alaska blackfish, and Pacific lamprey. Lake trout have been observed in Sally Lake and
Deadman Lake of the Upper Susitna watershed (Delaney et al. 1981a), but have not been
observed in the mainstem Susitna or tributary streams. Pacific lamprey have been observed in
the Chuit River (Nemeth et al. 2010), which also drains into Cook Inlet. Northern pike is an
introduced species that has been observed in the Lower and Middle Susitna River Segments
(Rutz 1999; Delaney et al. 1981b).
Non-salmon species that exhibit anadromous life histories in the Susitna River include eulachon,
humpback whitefish, and Bering cisco. Dolly Varden may exhibit both anadromous and resident
freshwater life history forms (Morrow 1980); however, Dolly Varden in the Susitna River were
regarded primarily as a resident fish during studies conducted in the 1980s (FERC 1984). Other
species that can exhibit an anadromous life history include humpback whitefish, threespine
stickleback, Arctic lamprey, and Pacific lamprey (Morrow 1980). Northern pike are considered
an invasive species in the Susitna drainage and have spread throughout the system from the
Yenta drainage after being illegally introduced in the 1950s (Rutz 1999). Alaska blackfish
would also be considered an invasive species in this basin, and while not previously captured in
the Susitna River, may have been introduced.
Pacific salmon (all five species) were captured in the Lower and Middle Susitna River during the
1980s. Chinook salmon spawn exclusively in tributary streams (Thompson et al. 1986; Barrett
1985; Barrett 1984; Barrett et al. 1983); nearly all Chinook salmon juveniles out-migrate to the
ocean as age 1+ fish, and very few exit the system as fry. Coho salmon typically out-migrate to
sea as age 1+ or age 2+ fish. Because chum and pink salmon out-migrate to sea within a few
months of emergence, little is known about their dependence on the Susitna River. Most age 0+
sockeye salmon out-migrate from the Middle River. It has not been determined whether they rear
in the Lower River or if they go to sea at age 0+.
Existing fish and aquatic resource information appears insufficient to address the following
issues identified in the PAD (AEA 2011a):
F4: Effect of Project operations on flow regimes, sediment transport, temperature, and
water quality that result in changes to seasonal availability and quality of aquatic habitats,
including primary and secondary productivity. The effect of Project-induced changes
include stream flow, stream ice processes, and channel morphology (streambed
coarsening) on anadromous fish spawning and incubation habitat availability and
suitability in the mainstem and side channels and sloughs in the Middle River above and
below Devils Canyon.
F6: Potential influence of the proposed Project flow regime and the associated response
of tributary mouths on fish movement between the mainstem and tributaries within the
Middle Susitna River Segment.
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F7: Influence of Project-induced changes to mainstem water surface elevations July
through September on adult salmon access to upland sloughs, side sloughs, and side
channels.
F8: Potential effect of Project-induced changes to stream temperatures, particularly in
winter, changing the distribution of fish communities, particularly invasive northern pike.
Agency staff have also expressed concerns that over time (i.e., 50 years), historic salmon
spawning areas downstream of the Watana Dam site may become less productive due to
potential changes in habitat conditions, in particular those areas affected by sediment transport,
gravel recruitment, bed mobilization, and embeddedness. Further, understanding the timing of
migration of juvenile salmonids from natal habitats to rearing areas and from the Middle Susitna
River Segment to the Lower Susitna River Segment is important for assessing the potential
Project effects.
Site-specific knowledge of the distribution, timing, and abundance of fish in the Susitna River is
available from the results of surveys conducted by the Alaska Department of Fish and Game
(ADF&G) during the early 1980s using multiple sampling methods (AEA 2011a). The existing
information can provide a starting point for understanding the distribution and abundance of
anadromous and resident freshwater fishes in the Susitna River and understanding the functional
relationship with the habitat types present. However, any significant differences between current
abundance and distribution patterns and those observed during the 1980s need to be documented.
In addition to providing baseline information about aquatic resources in the Project area, aspects
of this study are designed to complement and support other fish and aquatic studies.
9.6.3. Study Area
The proposed study area encompasses the Susitna River from RM 61 upstream to the proposed
Watana Dam site (RM 184) (Figure 9.6-1). RM 61, near the confluence with the Yentna River,
approximates the upper extent of tidal influence and is the lower extent of the Characterization
and Mapping of Aquatic Habitats Study (Section 9.9).
9.6.4. Study Methods
This study will employ a variety of field methods to build upon the existing information related
to the distribution and abundance of fish species in the Middle and Lower Susitna River. The
following sections provide brief descriptions of study site selection, sampling frequency, the
approach, and suite of methods that will be used to accomplish each objective of this study.
Fish Distribution and Abundance Implementation Plan
Some details of the sampling scheme have been provided for planning purposes; however,
modifications may be appropriate as the results of 2012 data collection are reviewed. A final
sampling scheme will be developed as part of a detailed Fish Distribution and Abundance
Implementation Plan and will be submitted to FERC on March 15, 2013. Implementation plan
development will include (1) a summary of relevant fisheries studies in the Susitna River, (2) an
overview of the life-history needs for fish species known to occur in the Susitna River, (3) a
review of the preliminary results of habitat characterization and mapping efforts (Section 9.9),
(4) a description of site selection and sampling protocols, (5) development field data collection
forms, and (6) development of database templates that comply with 2012 AEA QA/QC
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procedures. The implementation plan will include the level of detail sufficient to instruct field
crews in data collection efforts. In addition, the plan will include protocols and a guide to the
decision making process in the form of a chart or decision tree that will be used in the field,
specific of sampling locations, details about the choice and use of sampling techniques and
apparatuses, and a list of field equipment needed. The implementation plan will address how
sampling events will be randomized to evaluate precision by habitat and gear type. The
implementation plan will also help ensure that fish collection efforts occur in a consistent and
repeatable fashion across field crews and river segments. Proposed sampling methods by
objective are presented below and in Table 9.6-2. Brief descriptions of each sampling technique
are provided in Section 9.6.4.4.
9.6.4.1 Study Site Selection
A nested stratified sampling scheme will be used to select study sites to cover the range of
habitat types. The habitat classification hierarchy, as described in Section 9.9.5.4.1 of the
Habitat Classification Study, will be composed of five levels representing the following: (1)
major hydraulic segment; (2) geomorphic reach; (3) mainstem habitat type; (4) main channel
mesohabitat; and (5) edge habitat (Table 9.9-4, Nested and tiered habitat mapping units and
categories).
Level 1 separates the Susitna River into three major hydrologic segments: Lower River (RM 61–
98), Middle River (RM 98–RM 184), and Upper River (RM 184–233). The Upper River
Hydrologic Segment consists of the mainstem Susitna River and its tributaries upstream of the
proposed dam (RM 184) and will partially be within the impoundment zone and subject to
Project operations that affect daily, seasonal, and annual changes in pool elevation plus the
effects of initial reservoir filling (Section 9.5). In contrast, the Middle and Lower Hydrologic
Segments include the mainstem downstream of the proposed dam will be subject to the effects of
flow modification and water quality from Project operations, which will diminish in the Lower
Segment below the Three Rivers Confluence (98.5).
Level 2 identifies unique reaches based on the channel’s geomorphic characteristics (established
from the Geomorphology Mapping Study). The Geomorphic Study Team will delineate the
Lower, Middle, and Upper Susitna River reaches into large-scale geomorphic river segments
with relatively homogeneous landform characteristics, including at generally decreasing scales:
geology, hydrology (inflow from major tributaries), slope, channel planform, braiding or
sinuosity index (where relevant), entrenchment ratio, channel width, and substrate size.
Stratification of the river into relatively homogeneous segments will facilitate relatively unbiased
extrapolation of sampled site data within the individual segments because sources of variability
associated with large-scale features will be reduced. Stratification will occur across geomorphic
reaches as much as possible but will be dictated by the distribution of habitat types present
within each reach. For example, based on preliminary geomorphic reach delineation, we would
expect to find multiple split main channel habitats in reaches MR 2, 6, and 8 but not in the more
confined and incised reaches that include Devils Canyon MR 3, 4, 5, and 7.
Level 3 classifies the mainstem habitat into main channel, off-channel, and tributary habitat
using a similar approach to the 1980s historical habitat mapping definitions (ADF&G 1983).
The main channel includes five mainstem habitat types, whereas the off-channel habitat will be
categorized into four types (Table 9.9-4). The 1980s classification of riverine habitats of the
Susitna River included six major mainstem habitat categories consisting of main channel, side
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channel, side slough, upland slough, tributaries, and tributary mouths (ADF&G 1984). These
mainstem habitat categories will be maintained in the 2012 classification system, but they are
further categorized into main channel, off-channel, and tributary. These will be expanded to
include five types of main channel (main channel, split main channel, multiple split main
channel, side channel, and tributary), and four types of off-channel (side slough, upland slough,
backwater, and beaver complex) (Table 9.9-4).
Level 4 will further delineate Level 3 main channel and tributary habitats into mesohabitat types
(pool, riffle, glide, and cascade) (Table 9.9-4). However, off-channel habitat will remain at
Level 3 (side slough, upland slough, backwater, and beaver complex).
The presence, distribution and frequency of these habitats vary longitudinally within the river
depending in large part on its confinement by adjoining floodplain areas, size, and gradient.
Thus, the fish sampling scheme also varies between the Middle and Lower River. Sampling in
the Lower River Segment will focus on relative abundance in Lower River Geomorphic Reach
LR1 (RM 61-98.5). This sampling will occur at 27 total sites (Figure 9.6-2) comprising three
replicates in each of the four categories of mainstem off-channel habitats (12), three replicates
within each of the four mainstem channel categories (12), and three replicates for tributary
mouths. Sampling within Lower River Geomorphic Reaches LR2-4 (RM 28-61) and tributaries
is not proposed at this time. It is assumed that the flow-related effects of Project operations on
mainstem and tributary habitats will be attenuated with increased distance from the dam an
increased flow inputs from tributaries and accretion. If results of the 2013 hydrology and
geomorphology studies indicate potential effects in Lower River Geomorphic Reaches 2-4 and
tributaries, this decision will be revisited during the Fish and Aquatic Technical Working Group
(TWG) process early winter of 2013-2014.
In the Middle River, fish distribution sampling will occur at 96 sites (Figure 9.6-3). The
number of replicates per habitat unit varies from three for mesohabitats within main channel,
split channel, and multiple split main channel to six for most other mainstem habitats (side
sloughs, upland sloughs, backwater habitats, beaver complexes, and tributary mouths). Due to
the number and varied nature of tributaries, sampling in 18 of the 62 Middle River tributaries is
proposed, and the team will select tributaries across the eight geomorphic reaches that represent
multiple stream orders; tributaries that have not been previously identified as supporting
anadromous fishes in the AWC will be prioritized. For relative abundance sampling, sampling
of 54 sites in the Middle River (Figure 9.6-4) is proposed. Sampling will occur throughout the
Middle River with the exception of Devils Canyon, where safety concerns prevent access.
Additionally, all “Focus Areas” will be sampled for relative abundance (Figure 9.6–5). Focus
Areas are sites in which a full complement of cross-disciplinary intensive studies will occur to
enhance the richness of the data. Focus Area sites are being selected based on a combination of
recent and historic data along with the professional judgment of the various technical teams. The
first selection criterion is to select one or more sites that are considered representative of the
stratum or larger river and that contain all habitat types of importance. A suite of criteria
includes, but is not limited to geomorphological, riparian/floodplain, fish presence, and habitat
characteristics; groundwater, ice, and water quality; and constraints such as safety
considerations, raptor nests, land ownership and access. Geospatial data for these individual
attributes will be overlain in the Geographic Information System (GIS) to assist in site selection.
Approximately 8 Focus Areas are anticipated for the Middle River as well as at least one study
site below the Three Rivers Confluence in the Lower River.
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Site selection includes completing the geomorphic reach delineation and habitat mapping tasks
first. One sampling site representative of each mesohabitat type (side slough, upland slough,
side channel, beaver pond, and tributary mouth) present will then be selected for sampling using
techniques to determine relative abundance. It is anticipated that 50 Focus Area sites will be
sampled (Figure 9.6-5; 10 Focus Areas x 5 habitat types); however it is likely that not all Focus
Areas will contain each habitat type, therefore stratification will be finalized after results of
habitat mapping have been completed in spring 2013.. In addition to technical considerations,
access and safety will be key non-technical attributes for site selection for all studies. This, too,
influenced site selection in the 1980s studies, and will certainly influence site selection in the
present studies.
Finally, winter sites will be selected based on information gathered from winter 2012–2013 pilot
studies at Whiskers Slough and Slough 8A (Section 9.6.4.5). At a minimum, attempts will be
made to sample at all Focus Areas. The farthest upstream sites will need to be accessed by air
travel; sites closer to Talkeetna may be accessed by snow machine. Safety and access are
important considerations for the selection of these sites. Sampling methodologies including, but
not limited to, under ice use of Dual Frequency Identification Sonar (DIDSON) and video
cameras, minnow traps, seines, trot lines, pit tags, and radio tags will be tested in 2012–2013.
9.6.4.2 Sampling Frequency
Sampling frequency will vary among seasons and sites based on specific objectives. Generally,
sampling will occur monthly at all sites for fish distribution and relative abundance surveys
during the ice-free season. At Focus Areas, sampling will occur monthly year-round and
biweekly after break-up through July 1 to characterize the movements of juvenile salmonids
during critical transition periods from spawning to rearing habitats. More information on
sampling frequency specific to each objective is presented in Table 9.6-2.
9.6.4.3 Fish Sampling Approach
The initial task of this study will consist of a focused literature review to guide selection of
appropriate methods by species and habitat type, sampling event timing, and sampling event
frequency. Anticipated products from the literature review include the following:
A synthesis of existing information on life history, spatial and temporal distribution, and
relative abundance by species and life stage.
A review of sampling strategies, methods, and procedures used in the 1980s fish studies.
Preparation of periodicity charts for each species within the study area (timing of adult
migration, holding, and spawning; timing of incubation, rearing, and out-migration).
A summary of mainstem Susitna River habitat utilization for each species, by riverine
habitat type (main channel, side channel, side slough, upland slough, tributary mouth,
tributary).
A summary of existing age, size, and genetics information.
A summary of distribution of invasive species, such as northern pike.
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Knowledge of behavior and life history of the target species is essential for effective survey
design. Selected fish sampling methods will vary based on habitat characteristics, season, and
species/ life history of interest. Timing of surveys depends on the objectives of the study and the
behavior of the target fish species. Since life stage-specific information is desirable, timing of
the survey must match the use of the surveyed habitat by that life stage.
9.6.4.3.1 Objective 1: Fish Distribution, Relative Abundance, and Habitat Associations
Two general approaches to fish sampling will be used. The first is focused on gathering data on
general fish distribution (presence/absence). This sampling involves a single pass with
appropriate gear types. To the extent possible, the selected transects will be standardized and the
methods will be repeated during each sampling event at a specific site to evaluate temporal
changes in fish distribution. The second sampling approach is to gather data on relative
abundance as determined by catch per unit effort (CPUE) density; complementary data on fish
size, age, and condition factor will also be collected. The selected transects and fish capture
methods (i.e., number of passes, amount of soak time) will be standardized such that it is
repeatable on subsequent sampling occasions. This approach will also emphasize the
identification of foraging, spawning, and overwintering habitats.
Task A: Fish Distribution Surveys
Fish distribution surveys will include monthly 1-pass sampling events during the ice-free seasons
with year-round monthly sampling in Focus Areas. Methods will be selected based on species,
life stage, and water conditions. Snorkeling and electrofishing are preferred methods for juvenile
fishes in clear water areas where velocities are safe for moving about in the creek. The use of
minnow traps, beach seines, set nets, and fyke nets will be employed as alternatives in deeper
waters and habitats with limited access, low visibility, and/or high velocities. For larger/adult
fishes, gillnets, seines, trotlines, hoop traps, and angling will be used along with the opportunistic
use of fishwheels in conjunction with the Salmon Escapement Study (Section 9.7).
Survey methods will likely vary for the different study areas in the Middle and Lower Susitna
River Segments. Whereas snorkeling, minnow trapping, backpack electrofishing, and beach
seines may be applicable to sloughs and other slow-moving waters, it is anticipated that
gillnetting, boat electrofishing, hoop traps, and trot lines may be more applicable to the
mainstem. The decisions as to what methods to apply will be made by field crews after initial
site selection in coordination with Fish Distribution and Abundance Study Lead and the Fish
Program Lead and in accordance with state and federal fish sampling permit requirements.
Access may also influence survey methods and will be determined after a reconnaissance visit to
the site early in the 2013 field season.
Lastly, methods will vary seasonally with the extent of ice cover. Methods for winter sampling
will be based on winter 2012–2013 pilot studies. Selected methods will potentially include
DIDSON, underwater video, minnow traps, e-fishing, seines, and trot lines.
Task B: Relative Abundance
Relative abundance surveys will include monthly multi-pass sampling events during the ice-free
seasons with year-round monthly sampling in Focus Areas. As mentioned above, methods will
be selected based on species, life stage, and water conditions. All methods will be conducted
consistent with generating estimates of CPUE that are meaningful and facilitate comparison of
counts or densities of fish over space and time. This includes calibration and quality control of
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methods and documentation of conditions that affect sampling efficiency—such as visibility,
water temperature, and conductivity—to ensure that a consistent level of effort is applied over
the sampling unit.
Task C: Fish Habitat Associations
In conjunction with Tasks 1 and 2, data will be collected for fish distribution and abundance by
habitat type. This task includes an analysis of fish presence, distribution, and density by
mesohabitat type by season. The information on fish habitat use will help identify species and
life stages potentially vulnerable to Project effects.
9.6.4.3.2 Objective 2: Seasonal Movements
Task A: Document the timing of downstream movement and catch for all fish species using
out-migrant traps.
Understanding the timing of migration from natal tributaries to the mainstem Susitna River and
from the Middle Susitna River Segment to the Lower Susitna River Segment is important for
assessing the potential effects of the proposed Project. Out-migrant traps (rotary screw traps,
inclined plane traps) are useful for determining the timing of downstream-migrating juvenile
salmonids and resident fish.
Historically, out-migrant traps were fished at Talkeetna Station (historical RM 103) during open
water periods from 1982 to 1985 (Schmidt et al. 1983; Roth et al. 1984; Roth and Stratton 1985;
Roth et al. 1986) and at Flathorn Station (historical RM 22.4) during 1984 and 1985 (Roth and
Stratton 1985; Roth et al. 1986). Data from the 1980s suggests that the majority of Chinook
salmon fry out-migrate from natal creeks by mid-August and redistribute into sloughs and side
channels of the Middle River or migrate to the Lower River (Roth and Stratton 1985; Roth et al.
1986).
A maximum of six out-migrant traps will be deployed. Up to three traps will be stationed in the
mainstem Susitna River to characterize downstream migratory timing. Specific locations will be
determined with input from the Fish and Aquatic TWG. Because Chinook salmon are
predominantly tributary spawners, out-migrant traps will also be deployed in tributary mouths
such as Portage Creek, Indian River, and Whiskers Creek. In addition to collection of data on
migratory timing, size at migration, and growth, out-migrant traps will also serve as a platform
for tagging juvenile fish (Objective 2, Task B), recapturing previously tagged fish, and collecting
tissue samples (Objective 7) to support the Genetic Baseline Study (Section 9.14).
Task B: Describe seasonal movements using biotelemetry.
Biotelemetry techniques will include radio telemetry and PIT technology. PIT tags will be
surgically implanted in small fish >60 mm to monitor movement and growth; radio transmitters
will be surgically implanted in adult fish of sufficient body size of selected species distributed
temporally and longitudinally in the Middle and Lower River.
PIT tag antenna arrays with automated data logging will be used at selected side channel, side
slough, tributary mouth, and upland slough sites to detect movement of tagged fish into or out of
the site. Additionally, swim-over antennas will be deployed on an experimental basis at five
sites prior to ice-over and maintained throughout the winter months. All juvenile Chinook
salmon of appropriate size will be PIT-tagged; other target species will be tagged based on
proximity to PIT antenna arrays with a goal of 1,000 tags per species per PIT tag array. Target
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species are juvenile salmonids and selected fish species such as rainbow trout, Dolly Varden,
humpback whitefish, round whitefish, northern pike, Arctic lamprey, Arctic grayling, and burbot.
Recaptured fish will provide information on the distance and time travelled since the fish was
last handled and changes in length (growth).
Radio-tagged fish will be tracked with monthly aerial surveys, by boat, and by snow machine in
conjunction with the Salmon Escapement Study. The goal is to implant 30 radio transmitters per
target species including Dolly Varden, humpback whitefish, round whitefish, northern pike,
Arctic grayling, burbot, and rainbow trout.
9.6.4.3.3 Objective 3: Early Life History
Task A: Describe emergence timing of salmonids.
In conjunction with the Intergravel Monitoring component of the Fish and Aquatics Instream
Flow Study (Section 8.5.4), salmon redds in selected side channels and sloughs will be
monitored on a monthly basis throughout the winter in Focus Areas. Because chum salmon and
sockeye salmon are the principal salmon species using side channels and side sloughs for
spawning in the Susitna River (Sautner et al. 1984), 1980s egg development and incubation
studies were conducted on these two species and focused on chum salmon. Studies included
monitoring of surface and intergravel water temperatures, egg development, spawning substrate
composition, and trapping of emergent fry.
Sample sites will be selected in known chum and/or sockeye salmon spawning locations within
Focus Areas. Because water temperature is the most important determinant of egg development
and the timing of emergence (Quinn 2005), a component of the Fish and Aquatics Instream Flow
Study (Section 8.5.4) will include continuous monitoring stations for collection of temperature
data. Following methods used in the 1980s, fyke nets will be used to capture emerging fry on a
biweekly basis beginning in mid-April in each of the monitored side channels.
Task B: Determine movement patterns and timing of juvenile salmonids from spawning to
rearing habitats.
Bi-weekly sampling of fish distribution (Objective 1, Task A) from ice-out through July 1 will
occur in Focus Areas to identify changes in fish distribution by habitat type. Sampling methods
will include snorkeling, seining, electrofishing, minnow traps, fyke nets, and out-migrant traps
(Objective 2, Task A). Biotelemetry cannot be used for this task because juvenile salmonids will
be too small to tag at this life stage.
Task C: Determine juvenile salmonid diurnal behavior by season.
Selected sloughs in Focus Area sites will be sampled based on results from the Winter 2012–
2013 Pilot Study comparing the efficacy of underwater video and DIDSON for fish observation.
A stratified random sampling program over a 24-hour period will be developed to observe
underwater activity and ultimately to identify juvenile overwintering behavior to support
stranding and trapping analyses. Holes will be drilled in the ice where no open leads exist in a
few select sloughs; fish observation apparatus will also be deployed in open leads with low
velocity at pre-determined observation points. This task will be implemented in conjunction
with the Intergravel Monitoring component of the Fish and Aquatics Instream Flow Study
(Section 8.5.4). Depending on the efficacy of underwater imaging techniques, they may be
adopted for use during the ice-free season at selected Focus Area sites. Alternatively, sampling
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stratified by time of day using various techniques including but not limited to downstream
migrant traps, seining, fyke nets, minor traps and possibly electrofishing will be used to
characterize the diurnal distribution of juvenile salmonids.
Task D: Collect baseline data to support the Fish Stranding and Trapping Study.
Susceptibility to stranding can vary with fish size and species. Based on a review of available
literature, the Washington Department of Fish and Wildlife (Hunter 1992) concluded that
salmonid fry smaller than 50 mm in length are most susceptible to stranding whereas larger life
stages (i.e., fingerlings, smolts, and adults), while also vulnerable, can be protected by less
restrictive ramping criteria. Related to this, size (or life stage) periodicity will dictate the
seasonal timing during which vulnerable size classes may be present in the varial
zone. Stranding and trapping susceptibility may also vary by species based on differences in
periodicity, as well as species-specific habitat preferences and behavior. The focus of this task is
to support the stranding and trapping component of the Fish and Aquatics Instream Flow Study
(Section 8.5.4). Fish distribution sampling will occur at Focus Areas and at representative
habitat units to identify seasonal timing, size, and distribution among habitat types for fish
(particularly < 50 mm). Electrofishing, seining, fyke nets, and minnow traps will be the primary
methods for collecting salmon fry. Additional fish size data from downstream migrant traps
(Objective 2, Task A) will help identify when fish exceed the 50-mm length threshold.
9.6.4.3.4 Objective 4: Document Winter Movements and Timing and Location of Spawning
for Burbot, Humpback Whitefish, and Round Whitefish
Radio-tags will be surgically implanted in up to 30 burbot, humpback whitefish, and round
whitefish. Fish capture methods include fishwheels, gillnets, hoop traps, and angling. Radio-
tagged fish will be tracked by air, boat, and snow machine (Section 9.6.4.4.12). Following
methods outlined by Sundet (1986), radio-tag locations will be pin-pointed in winter with snow
machines, and trot lines will be set in the area of the radio-tag to identify winter spawning
aggregations and capture additional fish. The gonadal development of each captured fish will be
examined to determine spawning status; the gonads for all sampling mortalities will be preserved
for laboratory examination. The timing and location of all captured fish will be documented.
9.6.4.3.5 Objective 5: Document the Seasonal Age Class Structure, Growth, and Condition
of Juvenile Anadromous and Resident Fish by Habitat Type
In conjunction with Objectives 1 and 3, all captured fish will be identified to species. Up to 100
per season per species per life stage will be measured to the nearest millimeter (mm) fork length,
and in Focus Areas up to 30 fish per species per site will be measured on a monthly basis.
Length frequency data by species will be compared to length-at-age data in the literature to infer
age classes. Recaptured PIT-tagged fish (Objective 2 Task B) will provide information on
changes in length and weight (growth). Recorded parameters in each habitat unit will include
number of fish by species and life stage; fork length; global positioning system (GPS) location of
sampling area, time of sampling, weather conditions, water temperature, water transparency,
behavior, and location and distribution of observations. In concert with Objective 3 Task D,
seasonal timing, size, and distribution of fishes among habitat types, particularly fish <50 mm,
will be used to support the Fish Stranding and Trapping Study.
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9.6.4.3.6 Objective 6: Document the Seasonal Distribution, Relative Abundance, and
Habitat Associations of Invasive Species (Northern Pike)
Northern pike were likely established in the Susitna River drainage in the 1950s through a series
of illegal introductions (Rutz 1999). The proliferation of this predatory species is of concern
owing to their effect on salmonids and other species such as stickleback. Rutz (1999)
investigated movements of northern pike in the Susitna River using radio telemetry and
investigated northern pike predation on salmonids by analyzing stomach contents of juveniles
captured with minnow traps. Both of these fish capture methods used by Rutz (1999) will be
used in the current study, as well as angling, to capture northern pike. The presence/absence and
habitat associations of northern pike and other invasive fish species will be documented in all
fish capture and observation sampling events associated with Objectives 1 and 2.
9.6.4.3.7 Objective 7: Collect Tissue Samples from Juvenile Salmon and All Resident and
Non-Salmon Anadromous Fish
In support of the Fish Genetic Baseline Study (Section 9.14), fish tissues will be collected
opportunistically in conjunction with all fish capture events. The target species and number of
samples are given in Section 9.14. Tissue samples include an axillary process from all adult
salmon, caudal fin clips from fish >60 mm, and whole fish <60 mm.
9.6.4.4 Fish Sampling Techniques
A combination of gillnet, electrofishing, angling, trot lines, minnow traps, snorkeling,
fishwheels, out-migrant trapping, beach seines, fyke nets, DIDSON, and video camera
techniques will be used to sample or observe fish in the Lower River and Middle River, and
moving in and out of selected sloughs and tributaries draining into the Susitna River. Selected
methods will vary based on habitat characteristics, season, and species/life history of interest.
All fish sampling and handling techniques described within this study will be selected in
consultation with state and federal regulatory agencies and sampling will be conducted under
state and federal biological collection permits. Limitations on the use of some methods during
particular time periods or locations may affect the ability to make statistical comparisons among
spatial and temporal strata.
9.6.4.4.1 Gillnets
Variable mesh gillnets (7.5-foot deep panels with 1-inch to 2.5-inch stretched mesh) will be
deployed. In open water and at sites with high water velocity, gillnets will be deployed as drift
nets, while in slow water sloughs, gillnets will be deployed as set (fixed) nets. Depending on
conditions, gillnets may be deployed in ice-free areas, and under the ice during winter months.
The location of each gillnet set will be mapped using hand-held GPS units and marked on high-
resolution aerial photographs. The length, number of panels, and mesh of the gillnets will be
consistent with nets used by ADF&G to sample the river in the 1980s (ADF&G 1982, 1983,
1984). To reduce variability among sites, soak times for drift gillnets will be standardized; all
nets will be retrieved a maximum of 30 minutes after the set is completed. The following
formula will be used to determine drifting time:
T = ([(set time + retrieval time)/2] + soak time)
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9.6.4.4.2 Electrofishing
Boat-mounted, barge, or backpack electrofishing surveys will be conducted using standardized
transects. Boat-mounted electrofishing is the most effective means of capturing fish in shallow
areas (<10 feet deep) near stream banks and within larger side channels. Barge-mounted
electrofishing is effective in areas that are wadeable, but have relatively large areas to cover and
are too shallow or inaccessible to a boat-mounted system. Backpack electrofishing is effective in
wadeable areas that are relatively narrow. The effectiveness of barge and backpack
electrofishing systems can be enhanced through the use of block nets. Electrofishing methods
will follow NMFS (2000) Guidelines for Electrofishing Waters Containing Salmonids Listed
Under the Endangered Species Act.
Sites will be selected carefully, because electrofishing may have limited success in swift, turbid,
or low conductivity waters. Suspended materials in turbid water can affect conductivity, which
may result in harmful effects on fish, especially larger fish due to a larger body surface in contact
with the electrical field. Sudden changes in turbidity can create zones of higher amperage, which
can be fatal to young-of-year fish as well as larger fish. Electrofishing in swift current is
problematic, with fish being swept away before they can be netted. Similarly, turbidity increases
losses from samples. Electrofishing will be discontinued immediately in a sampling reach if
large salmonids or resident fish are encountered.
Selection of the appropriate electrofishing system will be made as part of site selection, which
will include a site reconnaissance. In all cases, the electrofishing unit will be operated and
configured with settings consistent with guidelines established by Smith Root. The location of
each electrofishing transect will be mapped using hand-held GPS units and marked on high-
resolution aerial photographs. To the extent possible, the selected electrofishing system and
transects will be standardized and the methods will be repeated during each sampling period at a
specific site to evaluate temporal changes in fish distribution. Habitat measurements will be
collected at each site using the characterization methods identified in Section 9.9. Any changes
will be noted between sample periods. The electrofishing start and stop times and water
conductivity will be recorded. Where safety concerns can be adequately addressed,
electrofishing will also be conducted after sunset in clear water areas; otherwise, electrofishing
surveys will be conducted during daylight hours.
9.6.4.4.3 Angling
Angling with hook and line can also be an effective way to collect fish samples depending on the
target species. During field trips organized for other sampling methods, hook-and-line angling
will be conducted on an opportunistic basis using artificial lures or flies with single barbless
hooks. The primary objective of hook-and-line sampling will be to capture subject fish for
tagging (i.e., northern pike) and to determine presence/absence; a secondary objective will be to
evaluate seasonal fish distribution. Because it is labor- and time-intensive, angling is best used as
an alternative method if other more effective means of sampling are not available. Angling can
also be used in conjunction with other methods, particularly if information is required on the
presence and size of adult fish.
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9.6.4.4.4 Trot Lines
Trot lines can be an effective method for capturing burbot, rainbow trout, Dolly Varden,
grayling, and whitefish. Trot lines are typically long lines with a multitude of baited hooks and
are typically anchored at both ends and set in the water for a period of time. Trot lines can also
be used during periods of winter ice cover. Trot line sampling was one of the more frequently
used methods during the 1980s and was the primary method for capturing burbot; however, trot
lines are generally lethal. Trot lines will consist of 14 to 21 feet of seine twine with six leaders
and hooks lowered to the river bottom. Trot lines will be checked and rebaited after 24 hours and
pulled after 48 hours. Hooks will be baited with salmon eggs, herring, or whitefish. Salmon
eggs are usually effective for salmonids, whereas the herring or whitefish are effective for Trot
line construction and deployment will follow the techniques used during the 1980s studies as
described in ADF&G (1982). As per ADF&G Fish Resource Permit stipulations, all salmon
eggs used as bait will be commercially sterilized or disinfected with a 10-minute soak in a 1/100
Betadyne solution prior to use.
9.6.4.4.5 Minnow Traps
Minnow traps baited with salmon eggs are an effective method for passive capture of juvenile
salmonids in pools and slow-moving water (Bryant 2000). In reaches where both electrofishing
and snorkeling would be ineffective due to stream conditions such as deep, fast water, baited
minnow traps will be used as an alternative to determine fish presence. During the 1980s,
minnow traps were also the primary method used for capturing sculpin, lamprey, and threespine
stickleback. Minnow traps also captured rainbow trout and Arctic grayling. Minnow traps will
be baited with salmon roe, then checked and rebaited after 90 minutes following protocols
outlined by Bryant (2000). Between 5 and 10 minnow traps will be deployed, depending upon
the size of the sampling site. All fish captured will be identified to species, measured, and
released alive near the point of capture. As per ADF&G Fish Resource Permit stipulations, all
salmon eggs used as bait will be commercially sterilized or disinfected with a 10-minute soak in
a 1/100 Betadyne solution prior to use.
9.6.4.4.6 Snorkel Surveys
This survey technique is most commonly used for juvenile salmonid populations, but can also be
used to assess other species groups. Generally, snorkeling works well for detecting presence or
absence of most species. Limits occur when water is or deep due to the inability to see the fish,
or the water is too swift to safely survey (Dolloff et al. 1993, 1996). To get relative abundance
estimates, a closed population is needed within a single habitat unit, and block nets will be used
to prevent fish from leaving the unit (Hillman et al. 1992).
In stream channels with a width of less than 4 m, the survey will be conducted by a single
snorkeler viewing and counting fish on both sides of the channel, alternating from left to right
counts. In stream channels with a width greater than 4 m, the surveys will be conducted by two
snorkelers working side by side and moving upstream in tandem, with each individual counting
fish on one side of the channel. The counts from all snorkelers are then summed for the total
count for the reach sampled. This expansion estimate assumes that counts are accurate and that
snorkelers are not counting the same fish twice (Thurow 1994). Data will be recorded following
completion of the survey. Survey reaches will be snorkeled starting at the downstream end and
working upstream.
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Snorkel surveys will also be used in combination with other techniques to estimate relative
abundance. This use of snorkel surveys provides a calibration factor for the counting efficiency
of snorkel surveys compared to other methods such as electrofishing and seining (Dolloff et al.
1996).
For most of the snorkel surveys in this study, two experienced biologists will snorkel along
standardized transects in clear water areas during both day and night during each field survey
effort. Snorkelers will visually identify and record the number of observed fish by size and
species. The location of each snorkel survey transect will be mapped using hand-held GPS units
and marked on high-resolution aerial photographs.
9.6.4.4.7 Fyke/Hoop Nets
Fyke or hoop nets will be deployed to collect fish in sloughs and side channels with moderate
water velocity (< 3 feet per second). After a satisfactory location has been identified at each site,
the same location will be used during each subsequent collection period. The nets will be
operated continuously for up to two days. Each fyke net will be configured with two wings to
guide the majority of water and fish to the net mouth. The fyke nets will have 1/8-inch mesh, 1-
foot diameter hoops, and up to 4 hoops. Where possible, the guide nets will be configured to
maintain a narrow open channel along one bank. Where the channel size or configuration does
not allow an open channel to be maintained, the area below the fyke net will be checked
regularly to assess whether fish are blocked and cannot pass upstream. A live car will be located
at the downstream end of the fyke net throat to hold captured fish until they can be processed.
The fyke net wings and live car will be checked daily to clear debris and to ensure that captured
fish do not become injured. The location of the fyke net sets will be mapped using a hand-held
GPS unit and marked on high-resolution aerial photographs.
9.6.4.4.8 Hoop Traps
Commercially available hoop traps have been used successfully by ADF&G on the Tanana River
as a non-lethal method to capture burbot for tagging studies (Evenson 1993; Stuby and Evenson
1998). Two sizes of traps have been used. Small and large hoop traps are 3.05 m and 3.66 m
long, respectively. The small hoop trap has seven 6.35-mm steel hoops with diameters tapered
from 0.61 m at the entrance to 0.46 m at the cod end. The large trap has inside diameters
tapering from 91 to 69 cm with throat diameters of 36 cm. Each trap has a double throat that
narrows to an opening 10 cm in diameter. All netting is knotted nylon woven into 25-mm bar
mesh. Each trap is kept stretched open with two sections of PVC pipe spreader bars attached by
snap clips to the end hoops. Bernard et al. (1991) provides an account of the efficacy of the
small and large traps.
Hoop traps will be deployed in mainstem areas of lower velocity to capture burbot from late
August through early October for radio-tagging (Objectives 1, 2, and 4). Soak times will
generally be overnight, but not more than 12 hours (M. Evenson pers comm 2012). All burbot
captured will be weighed, measured, and released. Up to 30 radio-tags will be surgically
implanted in burbot spatially distributed throughout the Susitna River.
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9.6.4.4.9 Beach Seines
Beach seines are an effective method to capture fish in a wide variety of habitats and are most
effective in shallow water areas free of large woody debris and snags such as boulders. Seining
allows the sampling of relatively large areas in short periods of time as well as the capture and
release of fish without significant stress or harm. Repetitive seining over time with standardized
net sizes and standardized deployment in relatively similar habitat can be an effective way to
quantify the relative abundance of certain species over time and space, especially for small
juvenile migrating salmon (Hayes et al. 1996). Beach seines will be 4 feet in depth and 40 feet
in length, ¼-inch mesh (net body) with a 1/8-inch net bag; however, the actual length of seine
used will depend on the site conditions. Low water conditions may be sampled using a shorter
and shallower beach seine; as long as the area sampled is noted and the net is deep enough to fill
the water column, then comparisons can be made. The location fished will be mapped using
hand-held GPS units and marked on high-resolution aerial photographs. The area swept will be
noted. Repetitive seining over time with standardized nets and soak times in relatively similar
habitats can be an effective way to quantify the relative abundance of certain species over time
and space, especially for small juvenile migrating salmon. To the extent possible, the same area
will be fished during each sampling event; net sizes and soak times will be standardized.
9.6.4.4.10 Out-Migrant Traps
Rotary screw traps are useful for determining the timing of emigration by downstream-migrating
juvenile salmonids and resident fish (Objective 2). In the 1980s, out-migrant trapping occurred
at Talkeetna Station (RM 103) during open water periods from 1982 to 1985 to determine
migratory timing and size at migration to the Lower Susitna River throughout the time traps were
operating (Schmidt et al. 1983; Roth et al. 1984; Roth and Stratton 1985; Roth et al. 1986). Peak
catch often occurred during periods of high flows. Out-migrant traps were also fished at
Flathorn Station (RM 22.4) during 1984 and 1985.
Selection of rotary screw trap locations will occur with input from the Fish and Aquatic TWG
and will be based on specific species, the physical conditions at the selected sites, and logistics
for deploying, retrieving, and maintaining the traps. Up to six out-migrant traps will be
deployed. Three to four traps will be located in mouths of important tributary streams or
spawning areas such as Fog Creek, Kosina Creek, Portage Creek, Indian Creek, and possibly
Gold Creek and Whiskers Slough. The remaining two or three traps will be situated in the main
channel to describe the broad timing of out-migrants from all upstream sources. Flow conditions
permitting, traps will be fished on a cycle of 48 hours on, 72 hours off throughout the ice-free
period. Each trap will be checked at least twice per day.
9.6.4.4.11 Fishwheels
Fishwheels will primarily be deployed to capture anadromous salmon as part of the Adult
Salmon Escapement Study (Section 9.7). However, non-salmon species are occasionally
captured by fishwheel. Non-salmon species collected by fishwheel will provide additional data
to support the objectives of this study and will be used opportunistically as a source of fish for
tagging studies and tissue sampling.
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9.6.4.4.12 Remote Fish Telemetry
Remote telemetry techniques will include radio telemetry and PIT technology. Both of these
methods are intended to provide detailed information from relatively few individual fish. Radio-
tracking provides information on fine and large spatial scales related to the location, speed of
movement, and habitat utilization by surveying large areas and relocating tagged individuals
during aerial, boat, and foot surveys. The target species to radio-tag include Dolly Varden,
humpback whitefish, round whitefish, northern pike, Arctic grayling, burbot, and rainbow trout.
PIT tags will be surgically implanted in small fish >60 mm; radio transmitters will be surgically
implanted in adult fish of sufficient body size of selected species distributed temporally and
longitudinally throughout the Susitna River. The target species to PIT-tag include juvenile
salmonids and selected fish species such as rainbow trout, Dolly Varden, humpback whitefish,
round whitefish, northern pike, Arctic lamprey, Arctic grayling, and burbot. PIT tags can be
used to document relatively localized movements of fish as well as growth information from
tagged individuals across seasons and years. However, the “re-sighting” of PIT-tagged fish is
limited to the sites where antenna arrays are placed. To determine movement in and out of side
sloughs or tributaries requires that tagged fish pass within several feet of an antenna array,
thereby limiting its use to sufficiently small water bodies. To characterize growth rates, fish must
be recaptured, checked for a tag, and measured.
Radio Telemetry
The primary function of the telemetry component is to track these tagged fish spatially and
temporally with a combination of fixed station receivers and mobile tracking. Time/date
stamped, coded radio signals from tags implanted in fish will be recorded by fixed station or
mobile positioning. All telemetry gear (tags and receivers) across both studies will be provided
by ATS, Inc. (Advanced Telemetry Systems, www.atstrack.com).
The types of behavior to be characterized include the following:
Arrival and departure timing at specific locations/positions
Direction of travel
Residence time at specific locations/positions
Travel time between locations/positions
Identification of migratory, holding, and spawning time and locations/positions
Movement patterns in and between habitats in relation to water conditions (e.g.,
discharge, temperature, turbidity)
Locating radio-tagged fish will be achieved by fixed receiver stations and mobile surveys (aerial,
boat, snow machine, and foot). Fixed stations will largely be those used for the Salmon
Escapement Study. In addition, up to five additional fixed stations will be established at
strategic locations with input from the TWG. These stations will be serviced in conjunction with
the Salmon Escapement Study during the July through October period and during dedicated trips
outside this period. Fixed stations will be downloaded as power supplies necessitate and up to
twice monthly during the salmon spawning period (approximately July through October). The
Salmon Escapement Study will provide approximately weekly aerial survey coverage of the
study area (approximately July through October). At other times of the year, the frequency and
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location of aerial surveys will be at least monthly and bi-weekly during critical species-specific
time periods (e.g., burbot spawning). Telemetry surveys will also be conducted by boat, snow
machine, and on foot to obtain the most accurate and highest resolution positions of spawning
fish. Using the guidance of fixed-station and aerial survey data on the known positions of tagged
fish, specific locations of any concentrations of tagged fish that are suspected to be spawning
will be visited to obtain individual fish positions. Foot and boat surveys will be conducted
approximately July through October as part of the spawning ground and habitat sampling in the
Salmon Escapement Study. Spatial and temporal allocation of survey effort will be finalized
based on the actual locations and number of each species of fish tagged.
The fundamental reason for using radio telemetry as a method to characterize resident and non-
salmonid anadromous species is that it can provide useful information to address the overarching
goal of the study and several of its objectives. In particular, radio telemetry can provide data on
seasonal distribution and movement of the target fish throughout the range of potential habitats.
Relocation data from the radio telemetry component of this study will be used to characterize the
timing of use and degree of movements among habitats and over periods during which the radio-
tags remain active (potentially two or three seasons for large fish). This objective may be
achieved by the use of long-life tags (e.g., greater than one year) and shorter-life tags (e.g., three-
month tags) applied to appropriate-sized fish over time. In general, successful radio telemetry
studies use a tag weight to fish weight guideline of 3 percent (with a common range of 2 to 5
percent depending on the species). The range in size encountered for a particular species may be
broad enough to warrant the use of different sized tags with different operational life
specifications. Actual tag life will be determined by the appropriate tag for the size of the fish
available for tagging.
In this regard, the range in weights for the seven target species to be radio-tagged has been
estimated. Fish weights and the respective target weight of radio-tags (Table 9.6-3) were
calculated using existing or derived length–weight relationships for Alaska fish (Figure 9.6-6),
and length frequency distributions for Susitna River fish. This analysis illustrates that there is a
relatively broad range of potential tag weights (0.5 g to 81 g) that are necessary to tag each
species over the potential range in fish size. Further, it is evident that some life stages will
require tags with a relatively short (30- to 200-day) operational period (tag life).
The broad range in tag weight complicates the scope of the task in terms of technological
feasibility. In general, there is a preference for using coded tags because it allows the unique
identification of a hundred tags on a single frequency. Conversely, standard tags (not coded)
require a single frequency for each tagged fish to allow unique identification. The radio
telemetry industry provides a variety of equipment to match research needs, but there are always
trade-offs in terms of tracking performance and cost between different systems. This plan
intends to capitalize on the use of the existing telemetry platform (ATS telemetry equipment) to
sufficiently monitor the target species, but directly constrains the potential options for tagging
and monitoring. More specifically, the smallest ATS coded tag weighs 6 g and therefore
precludes application to all of the species at the lower portion of their most frequently occurring
size range (Table 9.6–3). For example, if fish need to weigh a minimum of 200 g to be tagged,
then Dolly Varden would be tagged only at its largest samples, and burbot would be tagged
almost across its entire range (Table 9.6–3) based on its respective length–frequency
distributions.
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The use of non-coded tags on the smaller fish would require the use of many frequencies (e.g.,
50–150) and an entirely separate array of receivers. Overall, tagging fish weighing less than 200
g would be expensive and logistically inefficient. The only viable option to cover the entire
range of fish sizes would be to use alternate vendors’ radio telemetry receivers and tags that use
coded technology through the entire range of tag sizes (e.g., Lotek Wireless).
Tags will be surgically implanted in up to 30 fish of sufficient body size of each species
distributed temporally and longitudinally throughout the Middle and Lower River. These fish
will be captured opportunistically during sampling events targeting adult fish and with directed
effort using a variety of methods. Preference will be given fish caught with more benign
techniques that cause minimal harm and stress to fish. The final spatial and temporal allocation
of tags will be determined after 2012 study results are available (i.e., preliminary fish abundance
and distribution). The tag’s signal pulse duration and frequency, and, where appropriate, the
transmit duty cycle, will be a function of the life history of the fish and configured to maximize
battery life and optimize the data collection. Larger tags can accommodate the greatest battery
life and therefore will be used when fish are large enough, but smaller, shorter-life tags will be
used across the range of body sizes.
PIT Tag Antenna Arrays
Half-duplex PIT tags either 12 mm in length or 23 mm in length will be used, depending upon
the size of the fish. Each PIT tag has a unique code that allows for identification of individuals.
Half-duplex tags have been selected over full-duplex tags due to the increased flexibility and
reduced cost of working with the Texas Instruments technology. Texas Instruments has recently
produced a smaller half-duplex tag (12 mm) comparable to the original full-duplex (11 mm) tag;
this will allow tagging of fish down to approximately 60 mm. Increased read distance and
reduced power consumption are additional advantages of the half-duplex tag. Recaptured fish
will provide information on the distance and time travelled since the fish was last handled and
changes in length (growth).
PIT tag antenna arrays with automated data logging will be used at selected side channel, side
slough, tributary mouth, and upland slough sites to detect movement of tagged fish into or out of
the site. A variety of antenna types may be used including hoop antennas, swim-over antennas,
single rectangle (swim-through) antennas, or multiplexed rectangle antennas to determine the
directionality of movement.
Up to 10 sites will be selected with input from the Fish and Aquatic TWG for deploying PIT tag
antenna arrays. Antennas will be tested in the Winter 2012–2013 Pilot Study and deployed
shortly after ice-out in 2013 (See Section 9.6.4.5). Data loggers will be downloaded every two to
four weeks, depending on the need to replace batteries and the reliability of logging systems.
Power to the antennas will be supplemented with solar panels.
PIT tag arrays will be tested in a 2012 pilot study. Assuming the pilot testing is successful,
swim-over antennas will be deployed at five sites prior to ice-over and will be maintained
throughout the winter months. Downloading of data and battery replacement every three to four
weeks, weather permitting, will be the objective during winter months. Depending on the
detectability of tags during the winter of 2012–2013 Winter Pilot Study, winter deployment of
antennas may be expanded during the two subsequent winter field seasons. Data on fish growth
and movements into and out of habitats will inform bioenergetics and trophic analysis modeling
in the River Productivity Study.
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All juvenile Chinook salmon of appropriate size will be PIT-tagged. For other target species, up
to 1,000 tags per species per PIT tag array will be tagged based on proximity to PIT arrays.
Target species are juvenile salmonids and selected fish species such as rainbow trout, Dolly
Varden, humpback whitefish, round whitefish, northern pike, Arctic lamprey, Arctic grayling,
and burbot.
9.6.4.4.13 DIDSON and Video Cameras
Pending results of the 2012–2013 winter pilot study, the use of DIDSON and video cameras is
proposed to survey selected sloughs and side channels. The sloughs will be the same as those
selected for the wintertime deployment of PIT tag antennas. The deployment techniques will
follow those described by Mueller et al. (2006). Mueller et al. (2006) found that DIDSON
cameras were useful for counting and measuring fish up to 52.5 feet (16 meters) from the camera
and were effective in turbid waters. In contrast, they found that video cameras were only
effective in clear water areas with turbidity less than 4 nephelometric turbidity units (NTU). In
addition to fish observations, video cameras may also be used to characterize micro-habitat
attributes such as the presence of anchor ice, hanging dams, macrophytes, structure, and
substrate type. Depending on the efficacy of underwater imaging techniques, they may be
adopted for use during the ice-free season at selected Focus Area sites.
DIDSON is a high-resolution imaging sonar that provides video-type images over a 29-degree
field of view and can thus be used to observe fish behavior associated with spawning, i.e.,
dynamic behavior that cannot be identified on the static side-scan images. To obtain high-
quality images of adult salmon, the maximum range will be limited to 15 meters (49 feet).
Within this field of view, evidence of spawning behavior, e.g., redd digging, chasing, and
spawning, will be clearly identifiable. Furthermore, on DIDSON images fish can be classified
by size category, e.g., <40 centimeters, 40–70 centimeters, >70 centimeters (<25 inches, 25–44
inches, >44 inches, respectively). Although this is not sufficient for definitive species
identification, it will allow recognition of smaller resident fish, medium-sized adult salmon, and
large Chinook salmon.
Underwater video imaging can record images in real-time over short time intervals and can
provide information on fish species presence/absence in the immediate vicinity. Video systems
can also be configured to record images for longer periods of time using time lapse or motion
triggered recorders. Although water clarity and lighting can limit the effectiveness of video
sampling, a distinct advantage of video over DIDSON is the ability to clearly identify fish
species. In clear water under optimal lighting, video can capture a much larger coverage area
than DIDSON (Mueller et al. 2006). Video is often combined with a white or infrared (IR) light
source especially under ice and in low light northern latitudes; however, lighting may affect fish
behavior. Since nighttime surveys will be required to identify possible diurnal changes in fish
behavior and habitat use, the video system will be fitted with IR light in the form of light-
emitting diodes that will surround the lens of the camera. Muller et al. (2006) reported that most
fish are unaffected by IR lights operated at longer wavelengths because it falls beyond their
spectral range. In addition, the video system will be equipped with a digital video recorder for
reviewing and archiving footage of fish observations.
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9.6.4.4.14 Fish Handling
Field crews will record the date, start and stop times, and level of effort for all sampling events,
as well as water temperature and dissolved oxygen at sampling locations. All captured fish will
be identified to species. Up to 30 individuals per species per life stage per site will be measured
to the nearest millimeter (mm) fork length. Sampling supplies will be prepared before sampling
begins. For example, the date, location, habitat type, and gear type recorded in log book,
beginning fish number in proper sequence, daily sample objective by gear type, and an adequate
live box and clean area should be available. To increase efficiency, fish should be sampled in
order in groups of ten, and the sample routine followed in a stepwise manner: (1) identify species
and life stage, (2) measure lengths, (3) remove tissue samples for genetic analysis, and (4) cut all
dead fish for accurate sex identification. Care will be taken to collect all data with a consistent
routine and to record data neatly and legibly.
For methods in which fish are observed, but not captured (i.e., snorkeling, DIDSON, and
underwater video), an attempt will be made to identify all fish to species. For snorkeling, fork
length of fish observed will be estimated within 40-mm bin sizes. When fish are captured
observations of poor fish condition, lesions, external tumors, or other abnormalities will be noted
if present. When more than 30 fish of a similar size class and species are collected at one time,
the total number will be recorded and a subset of the sample will be measured to describe size
classes for each species. All juvenile salmon, rainbow trout, Arctic grayling, Dolly Varden,
burbot, longnose sucker, and whitefish greater than 60 mm in length will be scanned for PIT tags
using a portable tag reader. A PIT tag will be implanted into up to 1,000 fish of these species per
PIT tag array that do not have tags and are in close proximity to an array and approximately 60
mm and larger. Radio transmitters will be surgically implanted in up to 30 fish of sufficient body
size of each species distributed temporally and longitudinally throughout the Susitna River.
In support of the bioenergetics modeling component of the River Productivity Study (Section
9.8), targeted fish species will be collected for dietary analysis. These species include juvenile
coho salmon, juvenile and adult rainbow trout, and juvenile and adult northern pike, as identified
in consultation with agencies and other licensing participants. A total of five fish per species/age
class per sampling site collection will be sampled for fish stomach contents, using non-lethal
methods. All fish will have fork length and weight recorded with the stomach sample. In
addition, scales will be collected from the preferred area of the fish, below and posterior to the
dorsal fin, for age and growth analysis.
Tissue samples will be collected opportunistically in conjunction with all fish capture methods
from selected resident and non-salmon fish to support the Genetic Baseline Study (Objective 7;
Section 9.14). Tissue samples include an axillary process from all adult salmon, caudal fin clips
from fish >60 mm, and whole fish <60 mm. The target number of samples, species of interest,
and protocols are outlined in Section 9.14.
The number of fish per species or species assemblage and the handling protocols will be
determined with input from the Fish and Aquatics TWG and the Subsistence Group for species
consumed by humans, and the Wildlife TWG for piscivorous furbearers and birds.
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9.6.4.5 Winter Sampling Approach
Over the 2012/2013 winter, pilot studies will be conducted at the Whiskers Slough (RM 101-
102) and Slough 8A (RM 125-126) Middle Segment Focus Area sites of the Susitna River.
These sites were selected based on their accessibility from Talkeetna, because they contain a
diversity of habitat types, and because sampling in the 1980s and 2012 revealed that these sites
were used for spawning as well as rearing by salmonids. Three winter pilot studies will be
initiated in 2012–2013 focusing on (a) intergravel temperature, D.O., and water level monitoring;
(b) winter fish observations using DIDSON and underwater video; and (c) winter fish sampling
techniques.
Overall study objectives for the winter pilot study include:
1. Evaluate the effectiveness and feasibility of winter sampling methods for each study
including: intergravel temperature, D.O. and water level monitoring, underwater fish
observations via DIDSON sonar and underwater video, and fish populations using
minnow traps, seines, electrofishing, trotlines, PIT tags, and radio tags.
2. Assess winter sampling logistics. This includes safety, sampling methods in different
habitat types under varying degrees of ice cover, transportation and access to and from
sample sites, travel time, and winter-specific gear needs.
3. Evaluate the feasibility of sampling during spring break up.
Develop recommendations for 2013–2014 study plans.
Intergravel Temperature Monitoring
For the intergravel temperature component (Section 8.5.4.5.1.2.1), a detailed sampling design
will subsequently be developed that will be based on a stratified random sampling approach.
Both Whiskers Slough and Slough 8A will be stratified into specific habitat types (Beaver
complex, backwater, side slough, upland slough, tributary mouth, mainchannel) within which 10-
12 candidate monitoring sites will be randomly selected. Special emphasis will be giving to
including areas with known fish spawning. Dissolved oxygen will be measured in conjunction
with intergravel temperature at one location at each of the two Focus Areas. To the extent
possible, locations with groundwater upwelling will be distinguished from seepage locations that
may represent lateral intergravel flow from mainstem Susitna River surface flow. Sites will
include areas of recent spawning activity as well as areas with no spawning activity. Depending
on individual site characteristics, temperature monitoring devices will be installed at locations of
1) groundwater upwelling, 2) bank seepage and lateral flow from mainstem, 3) mixing between
upwelling and bank seepage, 4) no apparent intergravel discharge, fish spawning, and 5) main
channel Susitna River flow.
At each intergravel temperature monitoring location, Hobo TidBit temperature probes will be
deployed at three separate gravel depths (5 cm, 20 cm, and 35 cm) corresponding to observed
burial depth ranges of chum and sockeye eggs (Bigler and Levesque 1985, DeVries 1997).
Intergravel temperature probes will be attached to stainless steel cable and inserted into the
gravel using a scour chain installation device (Nawa and Frissell 1993). Additional above gravel
temperature recorders will be co-located at a subset of the intergravel sampling sites. These
latter devices allow for the downloading of temperature data without removing the recorders
from the gravel and allow for the detection of differences between surface and groundwater
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temperature. The D.O. sensors (HOBO D.O. logger with optical sensor) will likewise be inserted
into the gravel to a depth of approximately 20 centimeters using a stainless steel cable. In
addition, a series of pressure transducers (Solinst level loggers) will be deployed at the upper and
lower ends of select side channel and slough habitats and in adjoining areas of the main channel
Susitna River to monitor water surface elevations and stage response with changes in main
channel stage. The final number and location of monitoring sites will vary depending on site
conditions and safety concerns.
The temperature, D.O., and pressure transducers will be deployed in January 2012 following the
chum and sockeye salmon spawning period and will be retrieved in April 2013 prior to ice break-
up. Data from the above gravel recorders will be downloaded on a monthly basis and will occur
concurrently with times specified as part of the under ice fish observation study.
Underwater Fish Observations
Under-ice fish observations will be made using DIDSON sonar and underwater video cameras.
The two systems will be run concurrently in tannic water to determine which method is more
effective for underwater fish observations in varying water clarity. Underwater video and
DIDSON sonar observations will be made during the January–April 2013 sampling. Video
sampling will occur in both slough and side channel habitats in the same general study sites as
the intergravel temperature recorders. Observation will take place in 5 locations in Whiskers
Slough and 6 locations in Slough 8A. A stratified random sampling program over a 24-hour
period will be developed to observe underwater activity during day and nighttime conditions and
ultimately to identify juvenile overwintering behavior to support stranding and trapping analyses.
In addition to fish observations, Habitat Suitability Criteria (HSC) sampling methods will be
used to characterize local habitat characteristics (velocity, water depth, substrate, cover, etc.)
throughout the winter at all observed fish locations. Water velocity and depth measurements will
be made either through the ice (ice holes) or in open water leads using a topset wading rod and
Price AA meter. Channel substrate composition will be visually characterized using a modified
Wentworth size scale. HSC measurements will only be collected at those fish observations
points where positive fish species identification and estimates of total length can be made.
Winter Fish Sampling Techniques
Winter fish sampling will employ multiple methods to determine which are most effective for
each fish species, life stage, and habitat type. Because sampling efforts will occur in both open
water and ice covered sites, methods will vary depending on conditions. In ice-covered sites the
primary sampling methods will be trotlines and minnow traps. In open water sites, the fish
capture methods will be baited minnow traps, electrofishing, and beach seines. Remote telemetry
techniques will include radio telemetry and PIT technology. Both of these methods need to be
tested for detectability of tags fish under ice cover.
All fish sampling will occur once a month from January through March 2013 and will be
coordinated with the intergravel temperature monitoring and the underwater fish observation
components.
Trot Lines
Trot lines will be used to capture resident fish species including burbot, whitefish, Arctic
grayling and possibly rainbow trout and Dolly Varden. This was the primary method for
sampling resident fish (mostly burbot and whitefish) used by ADF&G during the 1980s winter
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studies (Sundet 1986). Following methods outlined by ADF&G, trotlines will be 15 to 20 feet in
length with 6 hooks and leaders weighted to the bottom of the river. Holes will be drilled in the
ice with a two-man ice auger. Trot lines will be baited with salmon roe or herring and set for 24
hours at a time once a month from January through March. Trot lines will be set in main channel
sites at Whiskers Slough and at Slough 8A within slough (Figures 9.6-7 and 9.6-8). Sites will be
marked with a hand-held GPS to ensure that sites can be relocated and resampled during future
sampling events. All captured fish will be identified to species, measured for length, and. gonads
examined to determine spawning status. The gonads for all sampling mortalities will be
preserved for laboratory examination. Tissue samples will be collected from all captured fish
and sent to the ADF&G Conservation Genetics Lab for genetic analysis.
Minnow Traps
Minnow traps will be deployed in attempt to capture juvenile salmonids and other juvenile
resident fish species overwintering in mainstem and slough habitats. Minnow traps were a
common winter method utilized by ADF&G in 1980s and were found to be effective for
anadromous and resident juvenile fish species (Stratton 1986) but also were able to catch non-
target species such as stickleback, sculpin and lamprey. Minnow traps will be deployed in the
same holes drilled for trotlines, baited with salmon roe and set for 24 hours. Minnow traps will
be deployed at 8 sites at Whiskers Slough and 3 sites at Slough 8A monthly from January –
March 2013. Minnow trapping locations will be marked with hand-held GPS units in order to
resample the same habitats each month. All captured fish will be identified to species, measured,
and released to the stream unharmed.
Beach Seines
Beach seines will be used to collect a range of anadromous and resident fish species that may be
present in open-water habitats. Beach seines will be used in shallow, open-water reaches free of
woody debris and boulders and will be swept through the water walking upstream. Seines will
be 15 and 25 feet wide by 5 feet depth with ¼ inch mesh. Locations of the habitats seined will be
marked with hand-held GPS units such that transects are standardized and repeatable. Single
passes with beach seines will occur at multiple locations between sites on a monthly basis. All
fish captured by beach seining will be identified to species, measured for length, and returned to
the stream unharmed.
Electrofishing
Single-pass backpack electrofishing surveys will be conducted in open-water leads (i.e., sloughs
and side channels) in attempt to capture a range of anadromous and resident fish species. The
location of each electrofishing transect will be mapped using a hand-held GPS unit. The
electrofishing start and stop times and water conductivity will be recorded. To the extent
possible, the selected electrofishing sites and transects will be standardized and the methods will
be repeated during each sampling period at each specific site to evaluate temporal changes in fish
distribution. All captured fish will be identified to species, measured for length, and returned to
the stream unharmed.
PIT Tag Arrays
Using 12 and 23 mm PIT tags and a mobile antenna array, we will test PIT tag detection in
varying ice thickness. This pilot effort will help determine the maximum depth of ice that PIT
tags can be detected and inform future PIT tagging studies in 2013 and 2014. Holes will be
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drilled in the ice and PIT tags will be attached to floats at the end of a tethered fishing line and
allowed to drift down stream under the ice. The orientation of a PIT tag relative to the antenna
array field will affect the tag detection rate, so the position of all test PIT tags will be fixed
within the float for each test. Mobile antenna arrays will be used to determine the maximum ice
thickness and distance PIT tags can be detected.
Radio Tags
The primary function of the telemetry component is to track tagged fish spatially and temporally.
Radio telemetry is intended to provide detailed information from relatively few individual fish.
Locating radio-tagged fish will be achieved by fixed receiver stations and mobile surveys (aerial,
boat, snow machine, and foot). Although wintertime radio tracking of adult fish was
successfully completed during the 1980s studies, there is some question as to the limitations of
detecting radio tags under ice cover. The process for testing the detectability of radio tags will
follow similar methods as outlined above for testing PIT tags. Holes will be drilled in the ice
and radio tags will be attached to the end of a fishing line and allowed to drift down stream under
the ice. Mobile antenna arrays will be used to determine the maximum ice thickness and
distance radio tags can be detected.
9.6.5. Consistency with Generally Accepted Scientific Practices
This study plan was developed by fisheries scientists in collaboration with the Fish and Aquatic
TWG and draws upon a variety of methods including many that have been published in peer
review scientific journals. As such, the methods chosen to accomplish this effort are consistent
with standard techniques used throughout the fisheries scientific community. However,
logistical and safety constraints inherent in fish sampling in a large river in northern latitudes
also play a role in selecting appropriate methodologies. To describe the seasonal distribution,
relative abundance, and habitat associations of the various fish species in winter, alternative
methods involving snorkel and dive surveys were considered. These alternative methods were
dismissed based on safety concerns owing to potentially extreme cold temperatures and
remoteness of the sampling locations, and because sampling would most appropriately be
conducted at night.
9.6.6. Schedule
Initial data collection efforts for this multi-year study will begin with the Winter Pilot Study
(January-April 2013) and will continue through March 2015. The schedule allows for two open
water and three ice-over study seasons. The proposed schedule for the completion of the Study
of Fish Distribution and Abundance in the Middle and Lower Susitna River Segments is given
below and in Table 9.6-4:
Conduct Winter Pilot Studies to inform 2013/14 and 2014/15 efforts – January through
April 2013
Development of Implementation Plan and selection of study sites – January through
March 2013
Continuation of Field studies after FERC Study Plan Determination – May 2013 through
March 2015
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Refined methods for winter sampling methods based on results of Winter 2012-2013
Pilot Study – June 2013
Reporting of interim results – September 2013 and September 2014
Quality control check of geospatially-referenced relational database – December 2013
and December 2014
Data analysis – October to December 2013 and October to December 2014
Initial and Revised Study Reports on 2013 and 2014 activities – anticipated to be filed
during the first quarter of 2014 and 2015, one and two years, respectively, after the FERC
Study Plan Determination (February 2013)
Supplemental technical memorandum on winter 2014–2015 effort – May 2015
9.6.7. Relationship with Other Studies
Over the two-year study implementation phase, an iterative process of information exchange will
take place between interrelated studies that depend upon one another for specimen collection or
data (Figure 9.6-9). Planning milestones include: segment delineation (Q2 2012) from the
Geomorphology Study (Section 6.0), mesohabitat delineation (Q4 2012) from the Aquatic
Habitat Study (Section 9.9), and Focus Area selection (Q4 2012) by the interdisciplinary study
(Section 8.5) will aid in site selection and development of the detailed Fish Distribution and
Abundance in the Middle and Lower Susitna River Implementation Plan (Q1 2013). In addition
to review of historic studies, the intergravel temperature component of the ISF Study (Q1 2013;
Section 8.5) and the Winter Pilot Study (Q1 2013; Section 8.5 and 9.6.4.5) will aid with the
estimation of fry emergence timing and planning and development of the Fish Distribution and
Abundance in the Middle and Lower Susitna River Implementation Plan (Q1 2013). Delivery of
information on spawning site locations and fishwheel collections from the Salmon Escapement
Study (9.7) will occur in an iterative fashion during the migration and spawning seasons.
Data checked for quality on fish distribution from this study will be provided to many studies
including the Instream Flow Study (Section 8.5) in the fourth quarter of 2014 to validate fish
periodicity, habitat associations, and selection of target species for reach-specific analyses.
Additionally, data collected on movement patterns and growth will be delivered to the Fish and
Aquatics Instream Flow Study (Section 8.5) in the fourth quarter of 2014 to aid in the
identification of seasonal timing, size and distribution among habitat types for fish (particularly <
50 mm) in support of the stranding and trapping component. Distribution and abundance data
will be delivered to the Salmon Escapement Study (Section 9.7) in the fourth quarter of 2014
help validate and complement information from radio telemetry, fishwheel, and sonar
observations of adult salmon. Fish movement, habitat association, and growth data will provide
inputs for bioenergetics and trophic analysis modeling in the fourth quarter of 2014, a component
of the River Productivity Study (Section 9.8). Further, target species will be sampled iteratively
throughout the course of the study for fish stomach contents in support of bioenergetics modeling
(Section 9.8). The opportunistic collection of tissue samples will occur iteratively throughout the
course of the study and be coordinated with the Fish Genetics Study (Section 9.14). Information
gathered on fish distribution and abundance will be delivered to the Fish Harvest Study (Section
9.15) in the fourth quarter of 2014 to complement information about harvest rates and to better
understand commercial, sport, and subsistence fisheries. Fish collections and observations in
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conjunction with aquatic habitat characterization (Aquatic Habitat Study, Section 9.9) will occur
iteratively throughout the course of the study and aid in the development of fish and habitat
associations. In fourth quarter of 2014, fish collections will provide data on fish use in sloughs
and tributaries with seasonal flow-related or permanent fish barriers to better classify barrier or
corroborate the Fish Passage Barriers Study (Section 9.12).
9.6.8. Level of Effort and Cost
This is a multi-year study that will begin in early 2013 and end in March 2015. The study will
include two winter periods and two ice-free periods. Sampling will be conducted according to a
stratified sampling scheme designed to cover the range of habitat types with a minimum of six
replicates each. The level of effort at each sample site and sampling frequency will vary based
on tasks and objectives. The number and size of sample sites and sampling frequency require a
large-scale field effort and subsequent data compilation, quality assurance/quality control
(QA/QC), and analysis efforts. Generally:
Sampling will be conducted monthly during the ice-free seasons in all study sites and
year-round in Focus Area sites.
Sampling will be conducted bi-weekly from ice-out through July 1 in selected Focus
Areas to document seasonal movement patterns of juvenile salmonids from spawning to
rearing habitats.
Fish capture and observation methods may include snorkeling, seining, gillnetting,
minnow trapping, angling, trot lines, out-migrant traps, DIDSON, and underwater video
depending on stream conditions such as depth, flow, turbidity, target species, and life
stage.
Field crews will consist of two to four individuals, depending on the sampling method
used.
Sampling in remote areas requires helicopter, fixed-wing airplane, snow machine, and
boat support.
Radio-tracking of tagged fish includes 12 aerial surveys, and foot, boat, and snow
machine surveys as necessary.
Total study costs are estimated at $4,500,000.
9.6.9. Literature Cited
Adams, N.S., D.W. Rondorf, S.D. Evans and J.E. Kelly. 1998. Effects of surgically and
gastrically implanted radio transmitters on growth and feeding behavior of juvenile
chinook salmon. Trans. Am. Fish. Soc. 127:128-136.
ADF&G (Alaska Department of Fish and Game). 1981. Adult Anadromous Fisheries Project
ADF&G/Su Hydro 1981. Alaska Department of Fish and Game, Susitna Hydro Aquatic
Studies, Anchorage, Alaska. 467 pp.
ADF&G (Alaska Department of Fish and Game). 1982. Aquatic Studies Procedures Manual:
Phase I. Su-Hydro Aquatic Studies Program. Anchorage, Alaska. 111 pp.
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ADF&G (Alaska Department of Fish and Game). 1983. Aquatic Studies Procedures Manual:
Phase II - Final Draft 1982-1983. Alaska Department of Fish and Game. Su-Hydro
Aquatic Studies Program. Anchorage, Alaska. 257 pp.
ADF&G (Alaska Department of Fish and Game). 1984. ADF&G Su Hydro Aquatic Studies
May 1983 - June 1984 Procedures Manual Final Draft. Alaska Department of Fish and
Game. Su-Hydro Aquatic Studies Program. Anchorage, Alaska.
AEA (Alaska Energy Authority). 2011a. Pre-application Document (PAD): Susitna-Watana
Hydroelectric Project FERC Project No. 14241. December 2011. Prepared for the Federal
Energy Regulatory Commission, Washington, D.C.
AEA. 2011b. Aquatic Resources Data Gap Analysis. Prepared by HDR, Inc., Anchorage. 107
pp.
Barrett, B. M. 1985. Adult Salmon Investigations, May - October 1984. Alaska Department of
Fish and Game, Susitna Hydro Aquatic Studies, Anchorage, Alaska. 528 pp.
Barrett, B. M., F. M. Thompson, S. Wick, and S. Krueger. 1983. Adult Anadromous Fish
Studies, 1982. Alaska Department of Fish and Game, Susitna Hydro Aquatic Studies,
Anchorage, Alaska. 275 pp.
Bernard, D. R., G. A. Pearse, and R. H. Conrad. 1991. Hoop traps as a means to capture burbot.
North American Journal of Fisheries Management 11:91-104.
Bigler, J., and K. Levesque. 1985. Lower Susitna River Preliminary Chum Salmon Spawning
Habitat Assessment. Alaska Department of Fish and Game, Susitna Hydro Aquatic
Studies. 140 pp.
Bryant, M. D. 2000. Estimating Fish Populations by Removal Methods with Minnow Traps in
Southeast Alaska Streams. North American Journal of Fisheries Management 20:923-
930, 2000.
Delaney, K., D. Crawford, L. Dugan, S. Hale, K Kuntz, B. Marshall, J. Mauney, J. Quinn, K.
Roth, P Suchanek, R. Sundet, and M. Stratton. 1981a. Resident Fish Investigation on the
Upper Susitna River. Alaska Department of Fish and Game, Anchorage, AK. 157 pp.
Delaney, K., D. Crawford, L. Dugan, S. Hale, K Kuntz, B. Marshall, J. Mauney, J. Quinn, K.
Roth, P Suchanek, R. Sundet, and M. Stratton. 1981b. Resident Fish Investigation on the
Lower Susitna River Alaska Department of Fish and Wildlife, Anchorage, AK. 311 pp.
DeVries, P. 1997. Riverine salmonid egg burial depths: A review of published data and
implications for scour studies. Canadian Journal of Fisheries and Aquatic Sciences 54:
1685-1698.
Dolloff, C.A., D.G. Hankin, G.H Reeves. 1993. Basinwide estimation of habitat and fish
populations in streams. USDA Forest Service General Technical Report SE-GTR-83. 25
p.
Dolloff, A., J. Kershner, R. Thurow. 1996. Underwater Observation. Pp. 533-554 In Murphy
and Willis (eds), Fisheries Techniques, American Fisheries Society, Bethesda Maryland,
732 p.
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Evenson, M. J. 1993. Seasonal movements of radio-implanted burbot in the Tanana River
Drainage. Alaska Department of Fish and Game Fishery Data Series No. 93-47,
Fairbanks, AK. 35 pp.
FERC (Federal Energy Regulatory Commission). 1984. Draft environmental impact statement:
Susitna Hydroelectric Project. Appendices H and I, Volume 4. Applicant: Alaska Power
Authority, Anchorage, Alaska.
Hayes, D. B., C. P. Ferreri, and W. W. Taylor. 1996. Active fish capture methods. Pages 193–
220 in B. R. Murphy and D. W. Willis, editors. Fisheries techniques. American Fisheries
Society, Bethesda, Maryland.
Hillman, T. W., J. W. Mullan, J. S. Griffith. 1992. Accuracy of underwater counts of juvenile
chinook salmon, coho salmon, and steelhead. North American Journal of Fisheries
Management. 12:598-603.
Hunter, M. A. 1992. Hydropower Flow Fluctuations and Salmonids: A Review of the Biological
Effects, Mechanical Causes, and Options for Mitigation. Washington Department of
Fisheries, Olympia, Washington, 58 p.
Morrow, J.E. 1980. The freshwater fishes of Alaska. Alaska Northwest Publishing Co.,
Anchorage.
Mueller, R.P., R.S. Brown, H. Hop, and L. Moulton. 2006. Video and acoustic camera
techniques for studying fish under ice: a review and comparison. (16):213-226.
Nawa, K. R., C. A. Frissell. 1993. Measuring scour and fill of gravel streambeds with scour
chains and siding-bead monitors. North American Journal of Fisheries Management 13:
634-639.
Nemeth, M.J., A.M. Baker, B.C. Williams, S.W. Raborn, J. T. Preist, and S.T. Crawford. 2010.
Movement and abundance of freshwater fish in the Chuit River, Alaska, May
through July 2009. Annual Report, Anchorage, Alaska.
NMFS (National Marine Fisheries Service). 2012. Comments of the National Marine Fisheries
Service on the Pre-Application Document, Scoping Document 1, Study Requests for the
Suistna-Watana Hydropower Project P-14241-000. Letter to Federal Energy Regulatory
Commission. May 31, 2012.
NMFS. 2000. Guidelines for electrofishing waters containing salmonids listed under the
Endangered Species Act. 5 pp.
Quinn, TP. 2005. The behavior and ecology of Pacific salmon and trout. University Press,
Seattle. 320 p.
Roth, K.J., and M.E. Stratton. 1985. The Migration and Growth of Juvenile Salmon in the
Suistna River. Pages 207 In: Schmidt, D.C., S.S. Hale, and D.L. Crawford. (eds.)
Resident and Juvenile Anadromous Fish Investigations (May - October 1984). Prepared
by Alaska Department of Fish and Game. Prepared for Alaska Power Authority,
Anchorage, AK.
Roth, K.J., D.C. Gray, J.W. Anderson, A.C. Blaney, and J P. McDonell. 1986. The Migration
and Growth of Juvenile Salmon in the Susitna River, 1985. Prepared by Alaska
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Department of Fish and Game, Susitna Hydro Aquatics Studies. Prepared for Alaska
Power Authority Anchorage, Alaska. 130 pp.
Rutz, D.S. 1999. Movements, food availability and stomach contents of Northern Pike in
selected Susitna River drainages, 1996-1997. Alaska Department of Fish and Game
Fishery Data Series No. 99-5. Anchorage, Alaska. 78 pp.
Sautner, J.S., L.J. Vining, and L.A. Rundquist. 1984. An evaluation of passage conditions for
adult salmon in sloughs and side channels of the middle Susitna River. Pages 148 In:
Estes, C.C., and D.S. Vincent-Lang. (eds.) Aquatic Habitat and Instream Flow
Investigations (May - October 1983). Alaska Dept. Fish and Game. Susitna Hydro
Aquatic Studies, Anchorage, Alaska.
Schmidt, D.C., S.S. Hale, and D.L. Crawford. 1985. Resident and juvenile anadromous fish
investigations (May - October 1984). Alaska Department of Fish and Game, Anchorage,
Alaska. 483 pp.
Stratton, M.S. 1986 Report 2, Part 2: Summary of juvenile Chinook and coho salmon winter
studies in the middle Susitna River, 1984-1985. Alaska Department of Fish and Game,
Anchorage, Alaska.
Stuby, L. and M. J. Evenson. 1998. Burbot research in rivers of the Tanana River Drainage,
1998. Alaska Department of Fish and Game Fishery Data Series No. 99-36, Fairbanks,
AK. 66 pp.
Sundet, R.L. 1986. Winter Resident Fish Distribution and Habitat Studies Conducted in the
Susitna River Below Devil Canyon, 1984-1985. Report to Alaska Power Authority by
Alaska Department of Fish and Game, Susitna Hydro Aquatic Studies, Anchorage,
Alaska. 80 pp.
Thompson, F. M., S. Wick, and B. Stratton. 1986. Report No 13., Volume I ,Adult Salmon
Investigations: May - October 1985. Alaska Department of Fish and Game, APA
Document No 3412, Anchorage, Alaska. 173 pp.
Thurow, R.F. 1994. Underwater methods for study of salmonids in the Intermountain West. US
Dept of Agriculture, Forest Service, Intermountain Research Station. General Technical
Report INT-GTR-307. Odgen, Utah. 28 p.
USFWS (United States Fish and Wildlife Service). 2012. Scoping Comments, Recommendations
and Study Requests Notice of Intent to File License Applications; Filing of Pre-
Application Document; Commencement of Licensing Proceeding and Scoping; Request
for Comments on the Pre-Application Document and Scoping Document 1, and
Identification of Issues and Associated Study Requests for the Susitna-Watana Project
No. 14241-00. Letter to K.D. Bose of the Federal Energy Regulatory Commission. May
31, 2012.
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9.6.10. Tables
Table 9.6-1. Summary of life history, known Susitna River usage, and known extent of distribution of fish species
within the Lower, Middle, and Upper Susitna River Segments (from ADF&G 1981 a, b, c, etc.).
Common Name Scientific Name Life Historya Susitna Usageb Distributionc
Alaska blackfish Dallia pectoralis F U U
Arctic grayling Thymallus arcticus F O, R, P Low, Mid, Up
Arctic lamprey Lethenteron japonicum A,F O, M2, R, P Low, Mid
Bering cisco Coregonus laurettae A M2, S Low, Mid
Burbot Lota lota F O, R, P Low, Mid, Up
Chinook salmon Oncorhynchus tshawytscha A M2, R Low, Mid, Up
Chum salmon Oncorhynchus keta A M2, S Low, Mid
Coho salmon Oncorhynchus kisutch A M2, S, R Low, Mid
Dolly Varden Salvelinus malma A,F O, P Low, Mid, Up
Eulachon Thaleichthys pacificus A M2, S Low
Humpback whitefishd Coregonus pidschian A,F O, R, P Low, Mid, Up
Lake trout Salvelinus namaycush F U U
Longnose sucker Catostomus catostomus F R, P Low, Mid, Up
Northern pike Esox lucius F P Low, Mid
Pacific lamprey Lampetra tridentata A,F U U
Pink salmon Oncorhynchus gorbuscha A M2, R Low, Mid
Rainbow trout Oncorhynchus mykiss F O, M2, P Low, Mid
Round whitefish Prosopium cylindraceum F O, M2, P Low, Mid, Up
Sculpine Cottid M1f, F P Low, Mid, Up
Sockeye salmon Oncorhynchus nerka A M2, S Low, Mid
Threespine stickleback Gasterosteus aculeatus A,F M2, S, R, P Low, Mid
a A = anadromous, F = freshwater, M1 = marine
b O = overwintering, P = present, R = rearing, S = spawning, U = unknown, M2 = migration
c Low = Lower River, Mid = Middle River, Up = Upper River, U = Unknown
d Whitefish species that were not identifiable to species by physical characteristics in the field were called humpback by
default. This group may have contained Lake (Coregonus clupeaformis), or Alaska (Coregonus nelsonii) whitefish.
e Sculpin species generally were not differentiated in the field. This group may have included Slimy (Cottus cognatus),
Prickly (Cottus asper), Coastal range (Cottus aleuticus), and Pacific staghorn (Leptocottus armatus).
f Pacific staghorn sculpin were found in freshwater habitat within the Lower Susitna River Segment.
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REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-69 December 2012 Table 9.6-2. Proposed methods by objective, task, species, and life stage. Obj Task Species/ Life Stage Study Sites Proposed Methods by Season 1A Distribution Juvenile salmon, non-salmon anadromous, resident Focus Areas + representative habitat types Select Focus Areas (accessible) Ice Free Season: Single pass sampling Selection of methods will be site-specific, species-specific, and life-stage-specific. For juvenile and small fish sampling, electrofishing, snorkeling, seining, fyke nets, angling, DIDSON and video camera where feasible and appropriate. For adults, directed efforts with seines, gillnets, trot lines, and angling. To the extent possible, the selected transects will be standardized and the methods will be repeated during each sampling period at a specific site to evaluate temporal changes in fish distribution. Additional info from radio telemetry studies (Objective #2). Winter: Based on winter 2012-2013 pilot studies Potentially DIDSON, video camera, minnow traps, e-fishing, seines, and trot lines. 1B Relative abundance Juvenile salmon, non-salmon anadromous, resident Focus Area study sites + representative habitat types Multi-pass sampling To the extent possible, the selected transects will be standardized and the methods will be repeated during each sampling period at a specific site to evaluate temporal changes in fish distribution. Snorkeling, beach seine, electrofishing, fyke nets, gillnet, minnow traps, fishwheels, out-migrant traps, etc. 1C Fish habitat associations Juvenile salmon, non-salmon anadromous, resident Focus Area study sites+ representative habitat types Analysis of data collected under Objective 1: Distribution. Combination of fish presence, distribution, and density by mesohabitat type by season. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-70 December 2012 Obj Task Species/ Life Stage Study Sites Proposed Methods by Season 2A Timing of downstream movement and catch using out-migrant traps All species; juveniles At selected out-migrant trap & PIT tag array sites Out-migrant Traps: Maximum of 6. 2-3 Main channel to indicate broad timing of out-migrants from all upstream sources. 3-4 in tributary mouths and sloughs, such as Fog Creek, Kosina Creek, Portage Creek, Indian Creek and possibly Gold Creek and Whiskers Slough. Combine with fyke net sampling to identify key site-specific differences. Sampling in mainstem off-channel habitats downstream of tributaries with fyke nets, seines, and out-migrant traps Fishwheels (adults only) opportunistically in conjunction with the Salmon Escapement Study 2B Describe seasonal movements using biotelemetry (PIT and radio-tags) All species Ice-Free Season: PIT tags: tags opportunistically implanted in target species from a variety of capture methods in Focus Areas. Antenna arrays in up to 10 sites at selected side channel, side slough, tributary mouth, and upland sloughs in the Middle River and Lower River. Radio-tags surgically implanted in up to 30 individuals of sufficient body size of each target species distributed temporally and longitudinally. . Winter: Based on winter 2012-2013 pilot studies. Potentially DIDSON, video camera, minnow traps, electrofishing, seines and trot lines. Aerial tracking of radio-tags (adults). 3A Describe emergence timing of salmonids; Juvenile salmonids Select Focus Areas Bi-weekly sampling using fyke nets, seines, electrofishing and minnow traps in salmon spawning areas within Focus Areas. 3B Determine movement patterns and timing of juvenile salmonids from spawning to rearing habitats; Juvenile salmonids Focus Areas Focus on timing of emergence and movement of newly emergent fish from spawning to rearing areas or movement of juvenile fish <50 mm in winter (i.e., the post-emergent life stages most vulnerable to load-following operations) DIDSON or underwater video to monitor movement into or out of specific habitats 3C Determine juvenile salmonid diurnal behavior by season Juvenile salmonids Focus Areas Stratified time of day sampling to determine whether fish are more active day/night DIDSON and/or video camera methods to observe fish activity Potentially electrofishing and seining 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-71 December 2012 Obj Task Species/ Life Stage Study Sites Proposed Methods by Season 3D Collect baseline data to support the Stranding and Trapping Study Focus Areas + supplement with additional representative habitat types as necessary. Opportunistic support to ID seasonal timing, size and distribution among habitat types for fish <50 mm in length. Estimate presence/absence, relative abundance, and density using similar methods as Objectives 1A, 1B, 1C, and 2 for fish <50 mm Focus on slough and other mainstem off-channel habitats DIDSON, video camera, electrofishing, seines, out-migrant traps and fyke nets. Monthly measurements of fish size/ growth 4 Winter movements, timing, and location of spawning burbot, humpback whitefish, and round whitefish Mainstem habitats Radio-tags surgically implanted in up to 30 fish of sufficient body size of each species distributed temporally & longitudinally. To capture burbot for radio-tagging, use hoop traps late Aug-early Oct following methods by Evenson (1993). To capture whitefish for radio-tagging, use fishwheels opportunistically and directed efforts including angling, seines & gillnets. Use aerial & snow machine tracking of radio-tags to pinpoint winter aggregations of fish; sample these areas with trot lines (similar to 1980s). Trot lines are lethal sampling. Collect, examine, and preserve gonads to determine spawning status. 5 Document age structure, growth, and condition by season juvenile anadromous and resident fish All study sites for Obj 1B and Focus Areas Stock biology measurements- length from captured fish up to 100 individuals per season per species per life stage and up to 30 fish per month per species per habitat type in Focus Areas. Emphasis placed on juvenile salmonids <50mm. Opportunistically support Stranding and Trapping Study 6 Seasonal presence/absence and habitat associations of invasive species northern pike All study sites Same methods as #1 and #2 above. The presence/absence of northern pike and other invasive fish species will be documented in all samples Additional direct efforts with angling as necessary 7 Collect tissue samples to support the Genetic Baseline Study All All study sites in which fish are handled Opportunistic collections in conjunction with all capture methods listed above. Tissue samples include axillary process from all adult salmon, caudal fin clips from fish >60 mm, and whole fish <60 mm. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
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Table 9.6-3. Length and weight of fish species to be radio-tagged and respective target radio-tag weights.
All sizes Most likely to be caught
Species
Length
(mm) Weight (g)
Fish
Length
(mm)
Est.
Weight
Min (g)
Est.
Weight
Max (g)
Tag
Weight
of Min
(3%)
Tag
Weight
of Max
(3%)
Fish length
(mm) @ 200 g
weight
Arctic grayling 36–444 <1–830 120–420 18 705 0.5 21.2 270
Dolly Varden 30–470 <1–1,007 130–300 20 256 0.6 7.7 277
Round whitefish 23–469 <1–1,035 150–390 23 553 0.7 16.6 287
Rainbow trout 27–612 <1–3,327 180–480 96 1635 2.9 49.1 232
Humpback whitefish 30–510 <1–1,544 210–450 180 1141 5.4 34.2 219
Burbot 26–791 <1–3,532 300–510 186 931 5.6 27.9 307
Northern pike 83–713 5–2707 200-700 62 2700 1.9 81.0 296
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Table 9.6–4. Schedule for implementation of the Fish Distribution and Abundance in the Middle and Lower Susitna
River Study.
Activity
2012 2013 2014 2015
1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2Q
Winter Pilot Study
Study Site Selection
Develop and File Implementation Plan
Open Water and Winter Fish
Sampling --------
Data Entry
Preliminary Data Analysis
Initial Study Report Δ
Final Data Analysis
Updated Study Report ▲
Winter 2014-15 Technical Memo
Legend:
Planned Activity
----- Follow-up activity (as needed)
Implementation Plan
Δ Initial Study Report
▲ Updated Study Report
Winter 2014-15 Technical Memorandum
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REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-75 December 2012 Figure 9.6-2. Schematic showing strata by habitat type for relative abundance sampling for the Lower River. Note that level two stratification within geomorphic segment, is not depicted in this figure because not all habitat types will be present within each geomorphic segment in the Upper River. The selection of habitats to sample will be distributed across geomorphic segments as described in the Fish Distribution and Abundance in the Lower and Middle Susitna River Implementation Plan and in Section 9.6.4.1. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-76 December 2012 Figure 9.6-3. Schematic showing strata by habitat type for fish distribution sampling for the Middle River. Note that level two stratification within geomorphic segment, is not depicted in this figure because not all habitat types will be present within each geomorphic segment in the Upper River. The selection of habitats to sample will be distributed across geomorphic segments as described in the Fish Distribution and Abundance in the Lower and Middle Susitna River Implementation Plan and in Section 9.6.4.1. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-77 December 2012 Figure 9.6-4. Schematic showing strata by habitat type for relative abundance sampling for the Middle River. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-78 December 2012 Figure 9.6-5. Schematic showing strata by habitat type for relative abundance sampling in Focus Areas. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
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Figure 9.6-6. Existing or derived length-weight relationships for fish species to be radio-tagged.
0
200
400
600
800
1000
1200
1400
1600
1800
2000
0 100 200 300 400 500 600Weight (g)Length (mm)
RBTR DLVD
PIKE BRBT
RDWF HBWF
GRAY
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REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-80 December 2012 Figure 9.6.-7. Distribution of winter sampling sites in Slough 8A, Susitna River. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-81 December 2012 Figure 9.6-8. Distribution of winter sampling sites in Whiskers Slough, Susitna River. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-82 December 2012 Figure 9.6-9. Flow chart of study interdependencies for Fish Distribution and Abundance in the Middle and Lower Susitna River Study Plan. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
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9.8. River Productivity Study
9.8.1. General Description of the Proposed Study
The production of freshwater fishes in a given habitat is constrained both by the suitability of the
abiotic environment and by the availability of food resources (Wipfli and Baxter 2010). Algae
are an important base component in the lotic food web, being responsible for the majority of
photosynthesis in a river or stream and serving as an important food source to many benthic
macroinvertebrates. In turn, benthic macroinvertebrates are an essential component in the
processes of an aquatic ecosystem, due to their position as consumers at the intermediate trophic
level of lotic food webs (Hynes 1970; Wallace and Webster 1996; Hershey and Lamberti 2001).
Macroinvertebrates are involved in the recycling of nutrients and the decomposition of terrestrial
organic materials in the aquatic environment, serving as a conduit for the energy flow from
organic matter resources to vertebrate populations, namely fish (Hershey and Lamberti 2001;
Hauer and Resh 1996; Reice and Wohlenberg 1993; Klemm et al. 1990). In turn, nutrients and
energy provided by spawning salmon have the potential to increase freshwater and terrestrial
ecosystem productivity (Wipfli et al. 1998; Cederholm et al. 1999; Chaloner and Wipfli 2002;
Bilby et al. 2003; Hicks et al. 2005), and may subsidize otherwise nutrient-poor ecosystems
(Cederholm et al. 1999).
The significant functional roles that macroinvertebrates and algae play in food webs and energy
flow in the freshwater ecosystem make these communities important elements in the study of a
stream’s ecology. The operations of the proposed Project would likely affect one or more of the
factors that can affect the abundance and distribution of benthic algae and benthic
macroinvertebrate populations, which could ultimately affect fish growth and productivity in the
system. The degree of impact on the benthic communities and fish resulting from hydropower
operations will necessarily vary depending on the magnitude, frequency, duration, and timing of
flows, as well as potential Project-related changes in geomorphology, ice processes, temperature,
and turbidity. By investigating the current populations of algae, benthic macroinvertebrates, and
fish in the Susitna River and the trophic relationships between them, this study will generate
information about the current health and status of these populations throughout the varied
habitats in the Susitna River, and provide a better understanding on the availability and
utilization of food resources in the system. In addition, by applying what is known about the
effects of river regulation and hydropower operation on these populations in riverine
ecoysystems, AEA can begin to assess the potential impacts of Project operations on river
productivity in the Susitna River, as well as provide information to inform development of any
necessary protection, mitigation, and enhancement (PM&E) measures.
Study Goals and Objectives
The overarching goal of this study is to collect baseline data to assist in evaluating the effects of
Project-induced changes in flow and the interrelated environmental factors (temperature,
substrate, water quality) upon the benthic macroinvertebrate and algal communities in the
Middle and Upper Susitna River. Individual objectives that will accomplish this are listed
below.
1. Synthesize existing literature on the impacts of hydropower development and operations
(including temperature and turbidity) on benthic macroinvertebrate and algal
communities.
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2. Characterize the pre-Project benthic macroinvertebrate and algal communities with
regard to species composition and abundance in the Middle and Upper Susitna River.
3. Estimate drift of benthic macroinvertebrates in selected habitats within the Middle and
Upper Susitna River to assess food availability to juvenile and resident fishes.
4. Conduct a feasibility study in 2013 to evaluate the suitability of using reference sites on
the Talkeetna River to monitor long-term Project-related change in benthic productivity.
5. Conduct a trophic analysis to describe the food web relationships within the current
riverine community within the Middle and Upper Susitna River.
6. Develop habitat suitability criteria for Susitna benthic macroinvertebrate and algal
habitats to predict potential change in these habitats downstream of the proposed dam
site.
7. Characterize the invertebrate compositions in the diets of representative fish species in
relationship to their source (benthic or drift component).
8. Characterize organic matter resources (e.g., available for macroinvertebrate consumers)
including coarse particulate organic matter, fine particulate organic matter, and
suspended organic matter in the Middle and Upper Susitna River.
9. Estimate benthic macroinvertebrate colonization rates in the Middle Susitna Segment
under pre-Project baseline conditions to assist in evaluating future post-Project changes
to productivity in the Middle Susitna River.
9.8.2. Existing Information and Need for Additional Information
A number of evaluations of the benthic macroinvertebrate community were conducted on the
Susitna River in the 1970s and in the 1980s for the original Alaska Power Authority (APA)
Susitna Hydroelectric Project (Friese 1975; Riis 1975, 1977; ADF&G 1983; Hansen and
Richards 1985; Van Nieuwenhuyse 1985; Trihey and Associates 1986). ADF&G studies in the
1970s included sampling of macroinvertebrates using artificial substrates (rock baskets)
deployed for a set period of time to allow for colonization. Friese (1975) and Riis (1975) set a
total of eight rock baskets in Waterfall Creek, Indian River, and the mainstem Middle Susitna
River for 30 days during summer (July – September). Riis (1977) also deployed rock baskets in
the Susitna River near the mouth of Gold Creek for a colonization period of 75 days; however,
only two of seven baskets were retrieved. Results were limited to low numbers of invertebrates
per basket, identified to taxonomic family.
Studies conducted in the 1980s for the original APA Susitna Hydroelectric Project focused on
benthic macroinvertebrate communities in the sloughs, side channels, and tributaries of the
Middle Segment of the Susitna River from river mile (RM) 125 to RM 142 during the period
from May through October. Efforts included direct benthic sampling with a Hess bottom
sampler and drift sampling. Alaska Department of Fish and Game (ADF&G) efforts in 1982 and
1984 also involved collection of juvenile salmon in these side channels and sloughs, and an
analysis was conducted to compare gut contents with the drift and benthic sampling results
(ADF&G 1983; Hansen and Richards 1985). In addition, Hansen and Richards (1985) collected
water velocity, depth, and substrate-type data to develop habitat suitability criteria (HSC), which
were used to estimate weighted usable areas for different invertebrate community guilds, based
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on their behavioral type (swimmers, burrowers, clingers) in slough and side channel habitats.
Efforts in 1985 (Trihey and Associates 1986) expanded to include sampling at nine sites in the
Middle Susitna River Segment: three side channels, two sloughs, two tributaries, and two
mainstem sites.
Algal communities were periodically sampled and analyzed for chlorophyll-a at Susitna Station
from 1978 to 1980. In the 1980s, algae samples were collected as part of the APA Susitna
Hydroelectric Project water quality studies, with sampling conducted at Denali, Cantwell (Vee
Canyon), Gold Creek, Sunshine, and Susitna Station on the Susitna River, as well as on the
Chulitna and Talkeetna rivers (Harza-Ebasco 1985 as cited in AEA 2011). Analysis showed low
productivity (less than 1.25 mg/m3 chlorophyll-a) and indicated algal abundance was most likely
limited by high concentrations of turbidity (AEA 2011).
Baseline field data for benthic primary and secondary production was also collected in 1985, as
part of the Primary Production Monitoring Effort (Van Nieuwenhuyse 1985). Chlorophyll-a
(chl-a), and macroinvertebrates were collected from early April to late October 1985 from a
variety of off-channel and mainstem habitat sites. Early April sampling took place in an open-
water lead in Slough 8A, and revealed high macroinvertebrate densities (average 17,600
individuals/m2) comprised almost entirely of chironomid larvae, and chlorophyll-a densities
averaging 34.4 mg/m2. Sampling in early May in Slough 8A revealed macroinvertebrate
densities averaging 2,950 individuals/m2, again almost entirely chironomids, and chl-a densities
averaging 37mg/m2. Results from five mainstem habitat sites showed similar macroinvertebrate
numbers, with densities ranging from 393 to 8,820 individuals/m2 in May 1985, but with
considerably more diversity; chironomids accounted for an average of 53 percent of the density,
and only 8 percent of the macroinvertebrate biomass. Algae samples beyond May 1985 had not
been analyzed; therefore, no data were available for summer or fall. No sampling results were
given for summer macroinvertebrate sampling (June and July). August and September 1985
sampling showed low average densities at mainstem sites (44 – 164 individuals/m2), with large
increases occurring in October 1985 (1,729 – 7,109 individuals/m2). Average densities in Slough
8A in August 1985 remained similar to spring levels, at 2,851 individuals/m2, with a surge in
September 1985 (13,964 individuals/m2); again, chironomids represented over 80 percent of the
numbers. No further information or reports were available concerning the Primary Production
Monitoring Effort task.
Benthic macroinvertebrate information from the 1980s is focused on a limited number of
mainstem, side channel, and slough habitats located within a 17-mile reach of the Middle Susitna
River. Additional information is needed on mainstem benthic communities, as well as those in
side channel and slough habitats, within both the Middle and Upper Susitna River segments.
Benthic algae information needs to be collected in conjunction with the macroinvertebrates to
define their relationship in the river’s trophic system. To assess the impact of future hydropower
operations on the benthic communities within the Susitna River, additional information must be
collected through an increased sampling effort, including more sampling sites along the river in
relation to the distance both downstream from the proposed dam site and upstream from the
proposed Project reservoir area.
9.8.3. Study Area
The River Productivity Study will entail field sampling throughout the Upper Segment and
Middle Segment on the Susitna River (Table 9.8-1; Figures 9.8-1 through 9.8-2). The Upper
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Susitna River Segment is defined as the section of river above the proposed Watana Dam site at
RM 184 (Figure 9.8-1). Sampling in the upper portions of this segment above the proposed
reservoir (RM 233 – 260) will investigate the benthic communities that will be unaffected by the
Project. The Middle Susitna River Segment encompasses the 86-mile section of river between
the proposed Watana Dam site and the Chulitna River confluence, located at RM 98 (Figure 9.8-
2). Sampling activities within this segment will investigate the benthic communities that may be
affected by the Project and its regulated flows. Sampling will be conducted at various distances
from the proposed dam site to document longitudinal variability, and estimate the effects that the
proposed Project will have on benthos in the river system downstream. The Lower Susitna River
Segment, defined as the approximate 98-mile section of river between the Chulitna and
Talkeetna rivers confluence and Cook Inlet, will not be sampled in this study because the larger
influences of the Chulitna and Talkeetna rivers will attenuate Project operation effects, if any,
that would affect benthic communities on the mainstem Susitna River below the Three Rivers
Confluence.
AEA will reevaluate how far downstream Project operational significant effects extend based in
part upon the results of the Open-water Flow Routing Model (see Section 8.5.4.3), which is
scheduled to be completed in Q1 2013. Thus, an initial assessment of the downstream extent of
Project effects will be developed in Q2 2013 with input of the TWG. This assessment will
include a review of information developed during the 1980s studies and study efforts initiated in
2012, such as sediment transport (Section 6.5), habitat mapping (Sections 6.5 and 9.9),
operations modeling (Section 8.5.4.2.2), and the Mainstem Open-water Flow Routing Model
(Section 8.5.4.3). The assessment will guide the need to extend studies into the Lower River
Segment and if needed, will identify which geomorphic reaches will be subject to detailed
instream flow analysis in 2013. Results of the 2013 studies would then be used to determine the
extent to which the study should be modified to include sampling in the Lower River Segment in
2014.
9.8.4. Study Methods
This study will employ a variety of field methods to build upon the existing information related
to the benthic macroinvertebrate and algal communities in the Upper and Middle Susitna River.
The following sections provide brief descriptions of study site selection, sampling timing, the
approach, and methods that will be used to accomplish each objective of this study.
River Productivity Implementation Plan
This study includes a description of the sampling scheme. However, specific details regarding
site locations, timing, sampling devices, processing, and analyses will be dependent upon the
results of 2012 data collection efforts.
The final sampling scheme will be included in the River Productivity Implementation Plan,
which will be filed with FERC prior to March 15, 2013.
The Implementation Plan development will include: (1) a summary of relevant
macroinvertebrate and algal studies in the Susitna River, (2) an overview of the life-histories of
the target fish species in the Susitna River that are selected for the trophic analysis (Section
9.8.4.5.1), (3) a review of the preliminary results of habitat characterization and mapping efforts
(Section 9.9) and “Focus Areas” (Section 8.5.4.2.1.2), (4) a description of site selection
protocols, (5) a description of sampling protocols, (6) a description of sample processing
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protocols, (7) a discussion of data analysis methods, (8) development field data collection forms,
and (9) development of database templates that comply with 2012 AEA QA/QC procedures.
The implementation plan will include the level of detail sufficient to instruct field crews in data
collection efforts. In addition, the plan will include protocols and a guide to the decision-making
process in the form of a chart or decision tree that will be used in the field, specific sampling
locations, details about the choice and use of sampling techniques and apparatuses, and a list of
field equipment needed. The implementation plan will also help ensure that field collection
efforts occur in a consistent and repeatable fashion across field crews and river segments.
Proposed sampling methods by objective are presented below.
9.8.4.1. Synthesize existing information on the impacts of hydropower development
and operations (including temperature and turbidity) on benthic
macroinvertebrate and algal communities
Several reviews have been written on the effects that modified flows have on the benthic
communities residing below dams (Ward 1976; Ward and Stanford 1979; Armitage 1984; Petts
1984; Cushman 1985; Saltveit et al. 1987; Brittain and Saltveit 1989). A majority of these
reviews indicate that temperature and flow regimes are often the most important factors affecting
benthic macroinvertebrates below dams. The type of dam and its mode of operation will have a
large influence over the type and magnitude of effects on the receiving stream below. General
information on the effects of hydropower on riverine habitats, especially glacially-fed river
systems, as well as Project-specific information, will be reviewed and synthesized in a written
report. Specifically, AEA will prepare a written report that provides a literature review
summarizing relevant literature on macroinvertebrate and algal community information in
Alaska, including 1980s Susitna River data; review and summarize literature on general
influences of changes in flow, temperature, substrates, nutrients, organic matter, turbidity, light
penetration, and riparian habitat on benthic communities; and review and summarize the
potential effects of dams and hydropower operations, including flushing flows and load-
following, on benthic communities and their habitats. To the extent consistent with copyright
laws, electronic copies of all cited publications will be provided through the ARLIS library.
9.8.4.2. Characterize the pre-Project benthic macroinvertebrate and algal
communities with regard to species composition and abundance in the
Middle and Upper Susitna River
9.8.4.3. Benthic macroinvertebrate sampling
Macroinvertebrate sampling will be stratified by reach and mainstem habitat type defined in the
Project-specific habitat classification scheme (mainstem, tributary confluences, side channels,
and sloughs). To accomplish this objective, sampling will occur at six stations, each with three
sites (one mainstem site and two off-channel sites associated with the mainstem site), for a total
of 18 sites. Two stations will be located in the Upper Segment, above the proposed dam and
reservoir area (upstream of RM 223) (Table 9.8-1; Figure 9.8-1). In the Middle Segment, two
stations will be located between the dam site and the upper end of Devils Canyon, and two
stations will be located below Devils Canyon, within the Geomorphic Reach MR-6 (Table 9.8-1;
Figure 9.8-2). All stations established within the Middle Segment will be located at Focus Areas
established by the Instream Flow Study (Section 8.5.4.2.1.2), in an attempt to correlate
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macroinvertebrate data with additional environmental data (flow, substrates, temperature, water
quality, riparian habitat, etc.) for statistical analyses, and HSC/HSI development. Station and
site locations will be determined during the first quarter of 2013, and detailed in the River
Productivity Implementation Plan.
Three sampling periods will occur from April through October in both study years (2013–2014)
to capture seasonal variation in community structure and productivity. Seasonal periods are
tentatively scheduled for April through early June for Spring, late June through August for
Summer, and September through October for Autumn. Specific details on timing will be
provided in the River Productivity Implementation Plan. Timing of life history events for coho,
Chinook salmon, and rainbow trout (target species for Objective 5, Section 9.8.4.5.1) will be
consulted when scheduling sampling efforts.
Sampling will be conducted in riffle/run mesohabitats within mainstem and off-channel
macrohabitat types (i.e., tributary confluences, side channels, and sloughs). Higher flows may
inundate new shoreline substrates, which poses the risk of sampling in areas that are not fully
colonized. The shoreline bathymetry for each site will be evaluated such that changes in water
level due to increasing or decreasing flows must remain constant enough that the substrates
accessible for sampling will be continually inundated for a period of at least one month, to
facilitate colonization of those substrates.
Benthic macroinvertebrate sampling will be conducted using a stream-type sampler (Hess,
Surber, Slack) commonly used for other Alaskan benthic macroinvertebrate studies to allow for
comparable results; state and federal protocols (Hansen and Richards 1985; Barbour et al. 1999;
Klemm et al. 1990; Klemm et al. 2000; Carter and Resh 2001; Moulton et al. 2002; Peck et al.
2006), as well as methods used in the Susitna River studies in the 1980s, will be considered
when designing the sampling approach, which will be detailed in the River Productivity
Implementation Plan. Replicate samples (n=5) will be collected to allow for statistical testing of
results for short- and long-term monitoring. Measurements of depth, mean water column
velocity, mean boundary layer velocity (near bed), and substrate composition will be taken
concurrently with benthic macroinvertebrate sampling at the sample location for use in HSC/HSI
development in the instream flow studies. Water temperatures will be monitored hourly at sites
with submerged temperature loggers deployed at all sampling sites throughout the ice-free
season. Fine-scale (1 meter vertical and horizontal resolution) measurements of flow will be
recorded within a 5-m radius of selected sampling sites. Temperature and flow monitoring will
be coordinated with the Baseline Water Quality Study (Section 5.5) and the Instream Flow Study
(Section 8.5), and supplemental temperature loggers will be deployed if necessary to cover all
River Productivity Study sites.
In addition, floating emergence traps will be deployed at each site to determine both the timing
and the amount of adult insect emergence from the Susitna River (Cushman 1983). Adult
aquatic insect emergence mass is a product of aquatic insect production from the stream, and is
therefore a good surrogate for actual production (minus predation), and will be especially useful
for relative comparisons between river sections and years (personal communication, M. Wipfli,
University of Alaska-Fairbanks). Emergence traps will be checked and reset every month.
Trapped adults will be identified, enumerated, and weighed. Exact trap design will be
determined according to methods compatible with those used for other studies in comparable
streams/basins in Alaska, and will be detailed in the River Productivity Implementation Plan.
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Due to the prevalence of large woody debris in the Susitna River, woody snags, if present at a
sampling site, also will be sampled as a substrate strata for benthic macroinvertebrates, as
requested by the U.S. Fish and Wildlife Service (USFWS) (USFWS River Productivity Study
Request; May 31, 2012). Sampling methods for woody snags will be semi-quantitative, based
upon protocols established by the USGS (Moulton et al. 2002). Suitable woody snags will have
been submerged for an extended period of time so as to be clearly colonized. Woody snags to be
sampled will be removed from the water by using a saw and placed over a plastic bin or in a
bucket, and all benthic macroinvertebrates will be removed by handpicking, brushing, and
rinsing. The snags will be allowed to dry for a period of time so that missed organisms will
crawl out of the crevices and can then be collected. Snag sections sampled will be measured for
length and average diameter to determine surface area sampled. Each snag section will originate
from a separate snag, and therefore count as a separate, replicate sample.
In order to address the effects of changing flow patterns on benthic macroinvertebrates, algae
(Section 9.8.4.2.2), and benthic organic matter (BOM) (Section 9.8.4.8), baseline data will be
collected to assess the benthic community responses to storm events within side slough habitats.
Additional sampling will be conducted both before and after storm events that meet or exceed a
1.5-year flood event at two side slough sites, located in two separate Focus Areas in the Middle
River Segment between Portage Creek and Talkeetna (Section 8.5.4.2.1.2). Replicate samples
(n=5) will be collected at both the upstream and downstream ends of each slough, and will
include benthic macroinvertebrates, algae, and BOM. Sampling will be conducted for two storm
events per year. Specific details on locations and targeted flows will be based on information
from the Instream Flow (Section 8.5) and Geomorphology (Section 6.5) studies available in early
2013, and will be provided in the River Productivity Implementation Plan.
Benthic macroinvertebrate replicate samples collected will be stored in individual containers and
immediately preserved in the field with 95 percent ethanol (non-denatured). Samples will be
processed in a laboratory using methods compatible with those used for other studies in
comparable streams/basins in Alaska. State and federal protocols (Barbour et al. 1999; Major
and Barbour 2001; Moulton et al. 2002) will be considered when making decisions about the
sample processing protocols, including sub-sampling protocols and the taxonomic resolution of
specimen identifications. Sampling and processing methodology will be detailed in the River
Productivity Implementation Plan.
Results generated from the collections will include several descriptive metrics commonly used in
aquatic ecological studies, such as density (individuals per unit of area), taxa richness (both mean
and total), EPT taxa (i.e., Ephemeroptera, Plecoptera, Trichoptera) richness, diversity (H’),
evenness (J’), percent dominant taxa, the relative abundance of major taxonomic groups, and the
relative abundance of the functional feeding groups. In conjunction with the bioenergetics
modeling (Section 9.8.4.5.1), biomass estimates will be taken for primary invertebrate taxa
collected for benthic and emergence sampling. The fresh blotted wet mass of invertebrate taxa in
samples will be recorded, the samples will be oven dried at 60˚C until reaching constant mass,
and the dry mass will be recorded. For a select sub-sample of the collection, energy density (J /
g wet weight) will be estimated from the percent dry mass (dry mass / wet mass) of each sample
(Ciancio et al. 2007; James et al. 2012). Energy density will be determined separately for the
aquatic and terrestrial (adult) life-stages of each primary invertebrate taxon. For two selected
stations, benthic macroinvertebrates and organic matter in samples will then be utilized for stable
isotope analysis (Objective 5, Section 9.8.4.5.2).
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Data collected during this study will be compared to the results of 1980s studies (ADF&G 1983;
Hansen and Richards 1985; Van Nieuwenhuyse 1985; Trihey and Associates 1986) to evaluate
any differences between the historic and current community structure. In addition, any invasive
benthic macroinvertebrates identified in the sample collections will be identified and their
collection locations will be recorded using the Geographic Information System (GIS) (NAD 83).
9.8.4.4. Benthic algae sampling
Benthic algae sampling will be collected concurrently with benthic macroinvertebrate sampling
at all six stations (18 sites total) to allow for correlation between the two collections (Table 9.8-
1), plus the additional baseline sampling effort addressing the effects of changing flow patterns
on benthic communities in sloughs, as discussed in Section 9.8.4.2.1. Benthic algae sampling
will be conducted using methods compatible with other Alaska benthic algal studies, to allow for
comparison of results. Algal sampling methods will be based on the EPA’s field operations
procedures for periphyton single or targeted habitat sampling when designing the sampling
approach (Eaton et al. 1998; Barbour et al. 1999; Peck et al. 2006). Measurements of depth,
mean water column velocity, mean boundary layer velocity, turbidity, and substrate composition
will be taken concurrently with algae sampling at the sample location for use in HSC
development in the instream flow studies. Light availability will be measured at each sample
location with an underwater light sensor, to measure the photosynthetically active radiation
(PAR) available to the algal community. Turbidity measurements will also be taken at the site to
determine water clarity. Benthic algae samples will be processed in a laboratory, using methods
compatible with those used for other studies in comparable streams/basins in Alaska, considering
state and federal protocols (Eaton et al. 1998; Barbour et al. 1999; Moulton et al. 2002; Peck et
al. 2006) to determine sample processing protocols, including sub-sampling protocols. Algal
sampling and processing methods will be detailed in the River Productivity Implementation Plan.
Results generated from the collections would include both dry weight and chlorophyll-a, and
several descriptive metrics to describe the algal community; full details will be provided in the
River Productivity Implementation Plan. For two selected stations, portions of algal material
will then be utilized for stable isotope analysis (Objective 5, Section 9.8.4.5.2). In addition, any
invasive algae taxa identified in the sample collections will be identified and their locations will
be recorded using GIS (NAD 83).
9.8.4.5. Estimate drift of invertebrates in selected habitats within the Middle and
Upper Susitna River to assess food availability to juvenile and resident fishes
Invertebrate drift sampling will be conducted concurrently with benthic macroinvertebrate
sampling at all sites within the six established sampling stations to allow for comparisons
between the drift component and the benthic macroinvertebrate community, as well as revealing
the availability of terrestrial invertebrates to fish predation. Sampling will be conducted in
riffle/run habitats within the mainstem sites, and their associated off-channel habitat sites (Table
9.8-1).
Invertebrate drift sampling will be conducted using a drift net similar to those used for other drift
studies in Alaska to allow for comparison of results; state and federal protocols will be
considered (Keup 1988; Klemm et al. 2000). Drift sampling will be conducted during pre-dawn
hours, as a measure of drift that is available to feeding fish (Waters 1972; Brittain and Eikeland
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1988; Keup 1988). Sampling methods will involve collecting duplicate samples to allow for
statistical testing of results for short- and long-term monitoring (Klemm et al 1990; Klemm et al.
2000). Water velocity will be recorded with an in-net flow meter. Invertebrate drift samples will
be processed in a laboratory, using methods compatible with other studies conducted in
comparable streams/basins in Alaska. State and federal protocols (Barbour et al. 1999; Major
and Barbour 2001; Moulton et al. 2002) will be considered when making decisions about the
sample processing protocols, including sub-sampling protocols, taxonomic resolution of
specimen identifications, and length measurements for individual specimens. Samples at two
selected stations (one each in Upper and Middle segments) will be tested for the stable isotope
analysis task (Section 9.8.4.5.2). Organic matter (OM) content will be retained and analyzed by
size (coarse and fine particulate OM) as discussed in Section 9.8.4.8.
Results generated from these collections will include drift density, drift rate, and drift
composition. In conjunction with the bioenergetics modeling (Section 9.8.4.5.1), biomass
estimates will be taken for primary invertebrate taxa collected for drift sampling. The fresh
blotted wet mass of invertebrate taxa in samples will be recorded, the samples will be oven-dried
at 60˚C until reaching constant mass, and the dry mass will be recorded. For a select sub-sample
of the collection, energy density (J / g wet weight) will be estimated from the percent dry mass
(dry mass / wet mass) of each sample (Ciancio et al. 2007; James et al. 2012). Energy density
will be determined separately for the aquatic and terrestrial life stages of each primary
invertebrate taxon. For two selected stations, portions of terrestrial invertebrate composition and
organic matter in samples will then be utilized for stable isotope analysis (Objective 5, Section
9.8.4.5.2).
Data collected as part of this study will be compared to data from the benthic macroinvertebrate
collections (Section 9.8.4.2.1) and the fish dietary analysis (Section 9.8.4.7). In addition, drift
results will be compared to the results of 1980s drift studies (ADF&G 1983; Hansen and
Richards 1985; Trihey and Associates 1986) to evaluate any differences between the historic and
current drift components of the macroinvertebrate communities.
9.8.4.6. Conduct a feasibility study in 2013 to evaluate the suitability of using
reference sites on the Talkeetna River to monitor long-term Project-related
change in benthic productivity
Sampling sites will be established in the Talkeetna River in areas that are physically similar to
those sampled in the Middle Susitna River Segment, to ensure comparability. Sampling will be
conducted in riffle habitats within the mainstem, side channels, and sloughs. One station will be
established, with a mainstem site and two off-channel habitat sites associated with the mainstem
site. Benthic and drift sampling will occur during approximately the same periods as sampling in
the Middle Susitna River Segment (Objectives 2 and 3, Sections 9.8.4.2 and 9.8.4.3), with
seasonal sampling during 2013. Benthic macroinvertebrate, benthic algal, and drift sampling
methods and processing protocols will be identical to those used in sampling the Middle Susitna
River Segment (Objective 2, Section 9.8.4.2). In the first quarter of 2014, sampling results from
Talkeetna sites will be compared to results from similar sites in the Middle Susitna River
Segment to determine whether the Talkeetna River would serve as a suitable reference site.
Statistical analyses will test for similarities and significant differences between Talkeetna sites
and Middle Susitna Segment sites by comparing community compositions and a collection of
calculated metrics. Methods will be detailed in the River Productivity Implementation Plan, and
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may include ANOVA, MANOVA, cluster analysis using Non-Metric Multi-Dimensional Scaling
(NMDS) ordinatation with the Bray-Curtis Dissimilarity Coefficient, and/or other multivariate
ordination techniques (Principal Components Analysis, Canonical Correspondence Analysis).
Results indicating close similarities, or no significant differences, between sites on the two rivers
would indicate suitability as a reference. If suitable, sites on the Talkeetna River can be used in a
long-term monitoring program with Susitna River sites to help differentiate potential long-term
changes that are Project-related versus those occurring for other reasons outside Project
influence. Such a monitoring program would ideally collect multiple years of both pre-Project
and post-Project data.
9.8.4.7. Conduct a trophic analysis, using trophic modeling and stable isotope
analysis, to describe the food web relationships in the current riverine
community within the Middle and Upper Susitna River
9.8.4.8. Develop a trophic model to estimate how environmental factors and food
availability affect the growth rate potential of focal fish species under current
and future conditions
To complement the fish habitat suitability analysis (Section 9.8.4.6), which focuses on physical
habitat features, trophic models will be developed to incorporate the density and quality of prey
into an estimate of habitat quality. Growth rate potential models integrate knowledge of the
foraging capabilities and bioenergetic physiology of a consumer with field data on its physical
environment and prey base to quantify the values of different habitats (Brandt et al. 1992; Nislow
et al. 2000; Jensen et al. 2006; Farley and Trudel 2009). The currency of these models, growth
rate potential (GRP), is the expected growth rate of a consumer occupying a given habitat. For
salmon, juvenile growth is strongly correlated with early marine survival and overall stock
dynamics (Pearcy 1992; Beamish and Mahnken 2001; Moss et al. 2005; Duffy and Beauchamp
2011), making GRP a particularly valuable metric of freshwater habitat quality.
One drawback of typical GRP models is that modeled fish are often assumed to occupy a single
uniform habitat (e.g., Brandt and Kirsch 1993). However, real fish may be able to exceed the
growth rate predicted by these models by moving among nearby habitats to feed, rest, and digest.
For example, by regularly moving between habitats of differing temperatures, some sculpin can
increase their growth rates by as much as three-fold, relative to a strategy of using a single
habitat (Wurtsbaugh and Neverman 1988; Neverman and Wurtsbaugh 1994). The growth of
juvenile coho and Chinook salmon is relatively insensitive to the range of temperatures typically
found in Alaskan streams, suggesting that small temperature differences among habitats may not
substantially affect growth (Beauchamp 2009). However, thermal heterogeneity has a strong
influence on the growth of juvenile coho salmon in the Bristol Bay region, due to the short
growing season and the potential for faster-growing individuals to consume energy-rich salmon
eggs (Armstrong et al. 2010). Further, resident fishes such as rainbow trout can exploit thermal
variation patterns by moving from colder to warmer streams to prolong their access to salmon
eggs and carcasses during the summer (Ruff et al. 2011). Thus, the local movement patterns of
both juvenile salmon and non-anadromous resident fishes among habitat types within the Susitna
River study area could potentially have important consequences for their growth rates.
Growth rate potential models will be developed to quantify the effects of environmental
conditions and food availability on fish growth at each sampling location, while allowing for
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local movement among habitats. Due to the relatively data-intensive nature of GRP models, this
analysis will focus on two species: coho salmon and rainbow trout. Coho salmon will be
included due to their high ecological and economic value in the Susitna Basin and Cook Inlet.
Rainbow trout will be included as a representative resident species and a potentially important
competitor and predator of juvenile salmon. Importantly, detailed foraging parameters are
available for both species (e.g., Dunbrack and Dill 1984; Berg and Northcote 1985; Piccolo et al.
2007; Piccolo et al. 2008a, 2008b), enabling the development of well-supported foraging models.
The necessary bioenergetics model parameters are also available for both species (Stewart and
Ibarra 1991; Rand et al. 1993).
Species-specific GRP models for coho salmon and rainbow trout will couple a foraging model
(Fausch 1984; Hughes and Grand 2000; Hayes et al. 2007) with a Wisconsin bioenergetics
model (Kitchell et al. 1977; Hanson et al. 1997). The foraging models will take inputs of flow,
turbidity, and prey density and predict a consumption rate. The bioenergetics models will take
inputs of consumption, body size, water temperature, diet composition, and the energy density of
prey and predict a growth rate. Each GRP model will allow for the potential of local movement
among habitats within a sampling location to enhance growth rates. Optimal simulated
movement patterns will be estimated and compared with the observed movements documented
by the radio telemetry and PIT tagging components of the Fish Distribution and Abundance
Study (Section 9.6).
Preliminary growth models for each species will be developed using data from the 2013 field
season as well as from prior Susitna Basin studies. Initial model predictions of the growth
potential of particular sites will be tested by comparison with the observed growth and
distribution of fish captured in those sites. A sensitivity analysis will be conducted to identify
the most important parameters for further refinement (Beaudreau and Essington 2009). Field
sampling during 2014 will focus on improving estimates for these parameters.
In addition, a separate trophic analysis will determine how water temperature, food availability,
and food quality influence the growth performance of juvenile Chinook salmon in different
habitats. Mechanistic drift foraging models for Chinook salmon are not yet available to allow
the estimation of growth rate potential under changing conditions. However, field data and
bioenergetics analysis will allow useful comparisons of growth rates, consumption rates, and
growth efficiency (the growth achieved per gram of food consumed) among different habitats
under current conditions. To make these comparisons, a Wisconsin bioenergetics model
parameterized for Chinook salmon (Stewart and Ibarra 1991; Madenjian et al. 2004) will take
field inputs of body size, growth rate, water temperature, diet composition, and the energy
density of prey. The model will estimate the consumption rate and growth efficiency. These
metrics will be compared among habitats to determine whether growth is currently limited
primarily by water temperature, food consumption, or food quality in the study area, and whether
these limiting factors differ among habitats (McCarthy et al. 2009).
9.8.4.9. Conduct stable isotope analysis of food web components to help determine
energy sources and pathways in the riverine communities
Stable isotope analysis is a method which examines the naturally-occurring stable isotopes of
elements (typically carbon and nitrogen) stored in organic materials. The analysis is frequently
used to answer questions related to trophic structure and energy pathways within freshwater
ecosystems and the interfaces with marine and terrestrial ecosystems (Chaloner et al. 2002;
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Finlay and Kendall 2007). Carbon isotope ratios (δ13C) are indicators of an organism’s diet
because consumers tend to reflect the carbon isotope values of the food they consume, whereas
nitrogen isotopes (δ15N) indicate an organism’s trophic level because the heavier nitrogen
isotope accumulates in the consumer with each successive trophic transfer (approximately 3– 4
parts per thousand, according to DeNiro and Epstein 1981) (Chaloner et al. 2002). If food
resources move in a predictable manner through the food chains, these stable isotopes can be
used to trace the sources of productivity within aquatic food webs and the trophic position of
consumers, which can be essential information for understanding the food web dynamics or for
detecting responses to environmental and human-driven change (Chaloner et al. 2002; Finlay and
Kendall 2007).
Several recent studies have used stable isotopes to investigate the contribution of marine-derived
nutrients (MDN) from spawning salmon to freshwater ecosystems, and have estimated that
salmon can contribute 17–30 percent (Bilby et al. 1996) to > 50 percent (Kline et al. 1990) of the
nitrogen, and 23–40 percent (Bilby et al. 1996) of the carbon present in freshwater organisms.
Adult salmon incorporate rich marine nutrients during their time in the ocean and are thereby
enriched with the heavier isotopes of nitrogen and carbon, which they retain after entering fresh
water to spawn, as they do not feed in fresh waters, and therefore remain isotopically distinct
from terrestrially-derived organic material (Kline et al. 1990). Stable isotope analysis can be
used to trace MDN through freshwater ecosystems, and ultimately can be used to quantify the
contribution of marine-derived nitrogen or carbon to freshwater food webs (Kline et al. 1990;
Hicks et al. 2005).
To better understand the trophic relationships in the Upper and Middle Susitna River, a stable
isotope analysis will be conducted at two selected stations (with three sampling sites each), with
one in the Upper River Segment, and one in the Middle River Segment. Selection of these two
stations will be made in the initial sampling efforts in the second quarter, based on how
representative the site is in respect to the reach, and its suitability to provide ample materials for
testing. Tissue samples from multiple study components (benthic macroinvertebrates, benthic
algae, benthic organic matter, terrestrial invertebrates and organic matter in drift samples, salmon
carcasses, and fin clip samples from the fish diet analysis collections) at the sites within these
two stations will be collected for stable isotope analysis. Results will be used in conjunction
with the bioenergetics model (Section 9.8.4.5.1) to further explain the energy source pathways
and trophic relationships in the Susitna River food web.
9.8.4.10. Generate habitat suitability criteria for Susitna benthic macroinvertebrate and
algal habitats to predict potential change in these habitats downstream of the
proposed dam site
Habitat Suitability Index (HSI) models provide a quantitative relationship between numerous
environmental variables and habitat suitability. An HSI model describes how well each habitat
variable individually and collectively meets the habitat requirements of the target species and life
stage under the structure of Habitat Evaluation Procedures (USFWS 1980). Alternatively,
Habitat Suitability Criteria (HSC) curves are designed for use in the Instream Flow Incremental
Methodology to quantify changes in habitat under various flow regimes (Bovee et al. 1998).
HSC describes the instream suitability of habitat variables related only to stream hydraulics and
channel structure. Both models and habitat index curves are hypotheses of species–habitat
relationships and are intended to provide indicators of habitat change, not to directly quantify or
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predict the abundance of target organisms. For the Susitna-Watana Hydroelectric Project aquatic
habitat studies, HSC (i.e., depth, velocity, and substrate/cover) and HSI (i.e., turbidity, duration
of inundation, and dewatering) models will be integrated to analyze the effects of alternate
operational scenarios.
Literature-based draft HSC/HSI curves will be developed for benthic macroinvertebrate and
algae communities. Potential sources of information include the Internet, university libraries,
peer-reviewed periodicals, and government and industry technical reports. Special emphasis will
be given to the existing 1980s study (Hansen and Richards 1985) for applicable information and
methodology. Because benthic macroinvertebrate (BMI) and periphyton communities are
comprised of numerous taxa, the HSC/HSI curves will be developed for commonly used benthic
metrics (e.g., biomass, chlorophyll-a [algae], density, diversity, or dominant taxa) selected to
summarize and describe the communities. The selection of individual species of interest will
consider the dietary preferences of the target fish species selected for the trophic analysis
(Objective 5, Section 9.8.4.5.1). The review will also examine macroinvertebrate life histories,
behavior, and functional feeding groups to assist in grouping taxa into guilds as possible metrics.
Habitat suitability information will address BMI and algal responses to changes in depth,
velocity, substrate, turbidity, and frequency of inundation and dewatering.
Next, a histogram (i.e., bar chart) will be developed for each of the habitat parameters (e.g.,
depth, velocity, substrate, frequency of dewatering) using site-specific field observations (from
Objectives 2, Section 9.8.4.2, and Objective 9, Section 9.8.4.9). The histogram developed using
field observations from 2013 will then be compared to the literature-based HSI curve to validate
applicability of the literature-based HSI curve for aquatic habitat modeling. This stage will be
conducted by the third quarter of 2014.
As a final step TWG will confirm HSC/HSI curves for each benthic metric. Using a roundtable
discussion format, the TWG will review literature-based benthic community information and
site-specific data to develop a final set of HSC/HSI curves. These curves will be used in the
Instream Flow Study (Section 8.5) to define the relationship between habitat quantity and quality
for each of the selected benthic metrics under various operational scenarios. Analysis and
modeling efforts will be coordinated with the Instream Flow Study Team.
9.8.4.11. Characterize the invertebrate compositions in the diets of representative fish
species in relationship to their source (benthic or drift component)
In order to investigate and understand the trophic relationships within a river system and how
they ultimately relate to fish, it is critical to examine not only the food source (Objective 2,
Section 9.8.4.2) and its availability to fish via drift (Objective 3, Section 9.8.4.3), but also the
consumption by fish predators. Because both benthic macroinvertebrates and terrestrial
invertebrates are a primary food source for fish and other organisms (Wipfli 1997; Hershey and
Lamberti 2001; Allan et al. 2003), any significant disturbance to the benthic community and the
shoreline riparian vegetation has the possibility of affecting their predators. Therefore, it is
important to investigate the trophic relationship between fish and these food sources by
conducting a fish gut analysis and comparing results to drift and benthic macroinvertebrate data.
In support of the bioenergetics modeling (Objective 5, Section 9.8.4.5.1), fish species targeted
for dietary analysis will include juvenile coho salmon, juvenile Chinook salmon, and juvenile
and adult rainbow trout, as identified in consultation with the TWG. Fish collection sites will
correspond to all sites within the six sampling stations identified for the study (Table 9.8-1),
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benthic macroinvertebrate collection sites (both benthic, , and drift sampling, to allow for
comparison with the benthic macroinvertebrate community (Section 9.8.4.2.1) and drift
compositions (Section 9.8.4).
A total of eight fish per species/age class per sampling site collection will be sampled for fish
stomach contents, using non-lethal methods (Meehan and Miller 1978; Hyslop 1980; Bowen
1996; Kamler and Pope 2001). All fish will have fork length and weight recorded with the
stomach sample. In addition, scales will be collected from the preferred area of the fish, below
and posterior to the dorsal fin, for age and growth analysis (DeVries and Frie 1996). At two
selected sampling stations (one each in Upper Segment and Middle Segment), fin clips will be
obtained from five fish at each site for use in the stable isotope analysis (Section 9.8.4.5.2). The
fish collection methods and scheduled sampling efforts will be coordinated with the appropriate
fish study team (Fish Distribution and Abundance in the Middle and Lower Susitna River Study,
Section 9.6; Fish Distribution and Abundance in the Upper Susitna River Study, Section 9.5).
Methods for collecting fish specimens are included in Sections 9.5.4.3, and 9.5.4.3.
Fish gut content samples will be processed in a laboratory using methods compatible with studies
conducted in other comparable streams/basins in Alaska. State and federal protocols (Hyslop
1980; Bowen 1996; Barbour et al. 1999; Major and Barbour 2001; Moulton et al. 2002) will be
considered in determining the sample processing protocols, the taxonomic resolution of
specimen identifications, and data analysis approach. Data collected during this study will be
compared to the results of 1980s fish diet studies (ADF&G 1983; Hansen and Richards 1985) to
evaluate any differences between the historic and current fish diets. Additional details on
sampling and processing methodology and analysis will be described in the River Productivity
Implementation Plan.
9.8.4.12. Characterize organic matter resources (e.g., available for macroinvertebrate
consumers) including coarse particulate organic matter, fine particulate
organic matter, and suspended organic matter in the Middle and Upper
Susitna River
Organic matter materials serve as an important food resource to benthic macroinvertebrates,
serving as a conduit for the energy flow from organic matter resources to vertebrate populations,
such as fish (Hershey and Lamberti 2001; Hauer and Resh 1996; Reice and Wohlenberg 1993;
Klemm et al. 1990). Given the dominant characteristics of the Susitna River system (large, cold,
and turbid during the growing season), secondary productivity is not likely to be driven by
primary production or from the algal community within the system, but rather by allocthanous
inputs of organic material from the terrestrial environment. Benthic organic material is one of
the most important “interrelated environmental factors” influencing the macroinvertebrate
community, and damming the river will have significant consequences for the transport of
organic matter from the upper watershed. Therefore, to address the importance of organic matter
to productivity in this type of system, quantifying benthic organic matter as part of this study is
essential.
This organic matter exists as both fine particulate organic matter (FPOM) and coarse particulate
organic matter (CPOM). FPOM includes particles ranging from 0.45 to 1000 µm in size, and
can occur in the water column as seston, or deposited in lotic habitats as fine benthic organic
matter (FBOM) (Wallace and Grubaugh 1996). CPOM is defined as any organic particle larger
than 1 mm in size (Cummins 1974). In order to quantify the amounts of organic matter available
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in the Susitna River for river productivity, CPOM and FPOM (specifically FBOM) will be
collected concurrently with all benthic macroinvertebrate sampling, including the baseline
sampling effort addressing the effects of changing flow patterns on benthic communities in
sloughs (Objective 2, Section 9.8.4.2.1). Organic debris collected within each sample will be
retained after processing for organisms. In order to streamline the collection efforts, a net mesh
size of 250 µm for sampling devices will retain FPOM in the 250–1,000 µm size range for
analysis, as well as CPOM particles. Suspended FPOM (seston) will be collected from material
in invertebrate drift samples, utilizing the 250-µm mesh size for drift nets, as well (Objective 3,
Section 9.8.4.3). Organic matter retained after organism sorting and processing will be separated
from inorganic material, rinsed through sieves to separate particles into size classes, oven-dried
(60°C), and weighed. Results will be calculated as amounts of CPOM and FPOM per unit area
(g/m2 and g/m3, respectively). For the two selected stations, portions of the material will then be
utilized for stable isotope analysis (Objective 5, Section 9.8.4.5.2). Additional details on
sampling and processing methodology and analysis will be described in the River Productivity
Implementation Plan.
9.8.4.13. Estimate benthic macroinvertebrate colonization rates in the Middle Susitna
River Segment t under pre-Project baseline conditions to assist in evaluating
future post-Project changes to productivity in the Middle Susitna River.
Colonization is a process in which organisms move into and become established in new areas or
habitats (Smock 1996). In disturbed habitats, this process is more accurately called
recolonization. Numerous studies have shown that macroinvertebrates can rapidly colonize new
or disturbed substrates (Shaw and Minshall 1980; Ciborowski and Clifford 1984; Williams and
Hynes 1977; Townsend and Hildrew 1976; Miyake et al. 2003). The rate of recolonization is
dependent on several factors, including time of the year, substratum particle size, the structure of
the macroinvertebrate assemblages available to colonize at the time, and the distance of the
colonist assemblages from the new or disturbed area (Robinson et al. 1990; Smock 1996;
Mackay 1992).
Two additional factors, predicted as major post-Project effects, that may affect colonization rates
are changes in turbidity and temperature. In order to assess the influences of turbidity and
temperature on the benthic community colonization rates, a field study will be conducted for
both study years (2013 and 2014) to estimate potential benthic macroinvertebrate colonization
rates for four different habitat types that reflect these conditions in the Susitna River. Due to the
difficulty of isolating each of these conditions under natural conditions, colonization will be
examined under turbid/warm, clear/warm, turbid/cold, clear/cold conditions. Sampling locations
and scheduling will be determined after a review of 2012 study results, from both AEA studies,
as well as from data collected outside of AEA, and site reconnaissance to assess candidate sites.
Sets of three preconditioned artificial substrates will be deployed incrementally for set periods of
colonization time (e.g., 8, 6, 4, 2, and 1 week[s]) and then pulled simultaneously at the
conclusion of the colonization period. Artificial substrates will be deployed at two depths at
fixed sites along the channel bed. Benthic macroinvertebrate processing protocols will be
identical to those used in Objective 2 (Section 9.8.4.2.1). Specific details on site locations, the
choice of artificial substrates, and timing of colonization tests will be provided in the River
Productivity Implementation Plan.
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Colonization information will be compared with colonization results from similar river systems
and with post-Project colonization results. In addition, results will be utilized in HSC/HSI
development (Objective 6, Section 9.8.4.6), and in the varial zone modeling task in the Instream
Flow Study (Section 8.5.4.6.1.6) to assist in determining the potential Project effect of short-term
flow fluctuations, most commonly the result of hydroelectric power generation, on benthic
macroinvertebrates.
9.8.5. Consistency with Generally Accepted Scientific Practices
The methods described above have been developed in consultation with agency and Technical
Workgroup (TWG) participants. All data collection and processing efforts will follow state
(ADF&G) or federal (EPA, USGS) guidelines referenced throughout the study methods
discussion (Agradi 2006; Barbour et al. 1999; Bovee et al. 1998; Eaton et al. 1998; Keup 1988;
Klemm et al. 1990, 2000; Major and Barbour 2001; Moulton et al. 2002; Peck et al. 2006;
USFWS 1980). In addition, any laboratory analysis will be conducted by a state- or federally-
certified facility.
9.8.6. Schedule
The preliminary schedule for the river productivity study elements is presented in Table 9.8-2.
During 2013, the literature review summarizing the impacts of hydropower development and
operations on benthic macroinvertebrate and algal communities will be prepared and presented to
the TWG. Research, field sampling, and sample processing and analysis will begin in the latter
half of the first quarter of 2013, following FERC’s approval of the study plan. Field sampling at
the Susitna River sites and the Talkeetna River test reference sites for benthic
macroinvertebrates, algae, organic matter, drift, fish diet analysis, and stable isotopes will be
conducted for three seasonal sampling periods from April through October in both study years
(20132014). These seasonal periods are tentatively scheduled for April through early June for
Spring, late June through August for Summer, and September through October for Autumn
(Table 9.8-2), due to annual variability in the timing of seasons. Specific details on timing will
be provided in the River Productivity Implementation Plan. Two additional sampling events for
benthic macroinvertebrates, algae, and organic matter to capture responses to storm events will
occur during April through October. Exact timing is subject to storm event occurrences. Sample
processing of organisms and materials collected in the 2013 field efforts will require extensive
laboratory efforts, and will continue throughout the remainder of 2013 and into the first quarter
of 2014. Trophic analysis efforts will also begin in the latter half of the first quarter of 2013 and
continue throughout 2013 and 2014. The Initial Study Report summarizing these 2013 activities
will be issued within one year of FERC’s Study Plan Determination (i.e., February 1, 2013).
Results from the 2013 effort will be utilized in the effort to generate habitat suitability criteria,
which begin early in the first quarter of 2014. Second-year field sampling efforts, adhering to
the same tentative scheduling as in 2013, will resume in the latter half of the first quarter of
2014, with sample processing, data analysis, trophic analysis research continuing through the
fourth quarter. The Updated Study Report will be produced within two years of FERC’s Study
Plan Determination.
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9.8.7. Relationship with Other Studies
The flow of information into and out of the River Productivity Study is anticipated to occur over
the two year study period through an iterative process. The River Productivity Study is
interrelated to several AEA studies (Figure 9.8-3). The Instream Flow Study (Section 8.5),
Characterization and Mapping of Aquatic Habitat Study (Section 9.9), and the Geomorphology
studies (Sections 6.5 and 6.6) will provide useful information, expected by Q1 2013, to assist in
the site selection process. The Baseline Water Quality Study (Section 5.5) will provide useful
input information for analysis of river productivity for use in the trophic analysis (Section
9.8.4.5). The Upper (Section 9.5) and Middle and Lower River (Section 9.6) Fish Distribution
and Abundance studies will provide information on target fish species for the trophic analysis,
including life history event timing to assist in sampling scheduling and seasonal locations in Q1
2013 and Q1 2014, as well as throughout the 2013 and 2014 field seasons. The Fish Distribution
and Abundance studies will also coordinate with the collection of samples for gut content
analysis (Section 9.8.4.7) and stable isotope analysis (Section 9.8.4.5.2) throughout the field
seasons. Output information from the multiple objectives of the River Productivity Study will
provide additional input information to the trophic analysis, Objective 5, Section 9.8.4.5, of the
River Productivity Study as well as any water quality field measurements (e.g., temperature,
turbidity, and PAR data) collected to the Baseline Water Quality Study (Section 5.5) and site-
specific field observations from Objective 2 and Objective 9 for use in the Instream Flow
Study’s IFIM and varial zone models (Section 8.5.4.6). Information flowing out from the River
Productivity Study will be communicated with other Fish Progam Study Lead. Additional
formal data sharing also will occur among study after completion of QA/QC procedures and with
delivery of the Initial Study Report (Q1 2014) and Updated Study Report (Q1 2015).
9.8.8. Level of Effort and Cost
The initial cost estimate for completion of the nine study objectives described above is
$1,200,000. Efforts such as the literature review, trophic analysis (bioenergetics model and
stable isotope analysis), and HSC criteria development will be office-based studies. Collection
of benthic macroinvertebrates, algae, and organic matter, drift samples, and the analysis of fish
diets will require three extensive field efforts per year for the two study years. Adult emergence
sampling will require monthly to bi-weekly site visits from April through October to collect
samples and reset the traps. The colonization study will require frequent site visits each month
to deploy additional sets of samplers over the course of the study. A majority of the work effort
will take place in the laboratory to sub-sample, sort, and identify the macroinvertebrate and algae
samples, as well as to conduct the stable isotope analyses on the numerous sample components.
After sample processing, the remainder of the study effort will be office-based, consisting of data
entry, analysis, and synthesis and report writing.
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for drift-feeding juvenile coho salmon and steelhead. Environmental Biology of Fishes
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processes: Measures for assessment of ecosystem health. Pages 287-305 in D.M.
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REVISED STUDY PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9-130 December 2012
Prepared for the U.S. Fish and Wildlife Service, Anchorage, Alaska. Alaska Department
of Fish and Game. APA Document 1610
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FERC Project No. 14241 Page 9-131 December 2012
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Wipfli, M.S., and C.V. Baxter. 2010. Linking Ecosystems, Food Webs, and Fish Production:
Subsidies in Salmonid Watersheds. Fisheries 35(8):373-387.
Wipfli, M.S., J. Hudson, and J. Caouette. 1998. Influence of salmon carcasses on stream
productivity: response of biofilm and benthic macroinvertebrates in southeastern Alaska,
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migration in a larval fish. Nature 333(6176):846-848.
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REVISED STUDY PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9-132 December 2012
9.8.10. Tables
Table 9.8-1. Preliminary macroinvertebrate and algae sampling sites, stratified by reach and habitats. Refer to Figures
9.8-1 – 9.8-2 for locations of the preliminary sampling reaches and stations.
Sampling Reach Reach Description Number of Mainstem
Sites
Number of
Associated
Off-channel Sites1
Upper Segment
UR-1, -2, -3 Reference upstream of reservoir 2 4
Middle Segment
MR-1 Immediately below dam site 1 2
MR-2 Upstream of Devils Canyon 1 2
MR-6 Downstream of Devils Canyon 2 4
Susitna River Totals 6 12
Notes: 1 Side-channels, sloughs, tributary confluences associated with a mainstem sampling site.
Table 9.8-2. Preliminary schedule for River Productivity Study.
Activity 2013 2014 2015
1Q 2Q 3Q 4Q 1Q 2Q 3Q 4Q 1Q
Literature Review on Hydropower Impacts
Sampling benthic macroinvertebrate
communities, algal communities, and
organic matter.
Invertebrate drift sampling
Sampling Talkeetna for Reference Site
Feasibility Study
Trophic analysis with bioenergetics and
stable isotope analysis
Generate habitat suitability criteria
Conduct a fish gut analysis
Establish baseline colonization rates
Data Analysis and Reporting
Initial Study Report ∆
Updated Study Report
Legend:
Planned Activity
Tentatively scheduled sampling event
∆ Initial Study Report
▲ Updated Study Report
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REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-133 December 2012 9.8.11. Figures Figure 9.8-1. Upper Susitna River Segment, preliminary sampling reaches for the River Productivity Study. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-134 December 2012 Figure 9.8-2. Middle Susitna River Segment, with the Instream Flow Focus Areas under consideration for the four sampling locations proposed within Geomorphic Reach MR-6 for the River Productivity Study. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9-135 December 2012 Figure 9.8-3. Study interdependencies for River Productivity Study.20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
ATTACHMENT C
Study Request Crosswalk Tables
U.S. Fish and Wildlife Service
National Marine Fisheries Service
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1
December 14, 2012
The Honorable Kimberly D. Bose
Secretary
Federal Energy Regulatory Commission
888 First Street, N.E.
Washington, D.C. 20426
Re:Susitna-Watana Hydroelectric Project, Project No. 14241-000
Submission of USFWS and NMFS Study Requests Crosswalk Tables
Dear Secretary Bose:
Through this filing, the Alaska Energy Authority (AEA)is submitting written
“crosswalk” tables that compare the original study requests of the U.S. Fish and Wildlife
Service (USFWS) and National Marine Fisheries Service (NMFS)(collectively, the
Services), filed with the Federal Energy Regulatory Commission (Commission or FERC)
on May 31, 2012,with AEA’s Revised Study Plan (RSP) for the original license
application for the Susitna-Watana Hydroelectric Project, FERC Project No. 14241
(Project). These crosswalk tables have been prepared at the request of the Commission
Staff and the Services.
Concurrent with this filing, AEA is filing the RSP pursuant to the regulations of
the Commission,18 C.F.R. §5.13(a). The RSP includes 58 individual study plans,
organized into resource sections and by topic within each section. As detailed in RSP
Section 1.1, AEA has been working closely with licensing participants, including the
Services,over the last year to develop this study plan. Following AEA’s development of
the Proposed Study Plan (PSP)in July 2012, AEA continued to consult regularly with
licensing participants on the PSP, which led to AEA’s release of an interim draft RSP at
the end of October 2012. AEA’s responses to comments received during the numerous
Technical Workgroup and other meetings during the July through October period appear
in Appendix 3 of the RSP, and documentation supporting these comments (e.g., meeting
summaries, e-mail messages) appears in Appendix 4 of the RSP. With regard to
comments received after the interim draft RSP, the Appendix 1 sets forth AEA’s
responses to licensing participants’ written comments filed with the Commission after
November 1. As documented in the RSP and its appendices, AEA and licensing
participants have resolved the majority of study-related issues in the Integrated Licensing
Process.
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With respect to the Services, the attached crosswalk tables document how the
objectives and methodologies of the Services’ original study requests—dating back to
May 2012, prior to the PSP—have been addressed in the RSP. See RSP §1.1.4 n.9.
Specifically, the crosswalk tables identify the equivalent RSP sections where the
Services’ original study request objectives and methodologies have been substantially
incorporated into the RSP. In instances where the RSP does not substantially incorporate
an original study request objective or methodology submitted by one or both Services, the
crosswalk tables either: (1) provide AEA’s rationale for not incorporating the objective
or methodology; or (2) document, by reference to Appendix 1 of the RSP, how the
objective or methodology has been modified, resolved, or dropped from the study plan
through the collaborative efforts of the licensing participants following AEA’s filing of
the PSP.
AEA notes that the Services included references to their specific resource
management objectives in several of their study requests. While AEA did not incorporate
equivalent resource management objectives in the RSP, it intends to consider those
objectives in its Exhibit E Environmental Exhibit included in its License Application. As
part of its effort in developing its Exhibit E, AEA will undertake a broader, more
comprehensive integrated analys is of Project impacts in the timeframe leading up to its
preparation of the Preliminary Licensing Proposal/Draft License Application,and
continuing through its filing of the final License Application. The integrated resource
analysis envisioned will involve the assimilation of individual study results, identification
and understanding of issues and impacts across resources, and an assessment of how
those impacts, and potential protection, mitigation, and enhancement measures to address
those impacts, might be influenced by elements of other resource areas. This analysis
will rely on a variety of analyses and computational models, at appropriate levels of
quantification, to compare various “with Project” scenarios to the base case “without
Project” conditions. AEA looks forward to interactive engagements with the Services
and other licensing participants, starting in early 2015 following the filing of the Updated
Study Report, in developing and conducting this integrated resource analysis. Through
these engagements, AEA anticipates that the Services’ resource management objectives
will be comprehensively analyzed based upon study results.
If you have any questions regarding this matter or need additional information,
please do not hesitate to contact the undersigned at wdyok@aidea.org or (907) 771-3955.
Sincerely,
Wayne Dyok
Project Manager
Alaska Energy Authority
Attachments
cc: Distribution List (w/o Attachments)
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ATTACHMENT 1
CROSSWALK TABLE BETWEEN
U.S. FISH AND WILDLIFE SERVICE STUDY REQUESTS
(MAY 31, 2012)
AND
ALASKA ENERGY AUTHORITY REVISED STUDY PLAN
(DECEMBER 14, 2012)
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USFWS | Study Request No. 11: River Productivity Study
USFWS Study Request Enclosure No. 11:
River Productivity Study
Study Objectives
Requested Study Objectives RSP Equivalent AEA Explanation
11.3.1: Develop a white paper on the
impacts of hydropower development and
operations (including temperature and
turbidity) on benthic macroinvertebrate
and algal communities in cold climates.
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
11.3.1: Characterize the pre-project benthic
macroinvertebrate and algal communities
with regard to species composition and
abundance in the lower, middle and upper
Susitna River.
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
See also AEA’s response to comment
RIVPRO-26.
11.3.1: Estimate drift of benthic
macroinvertebrates in habitats within the
lower, middle and upper Susitna River to
assess food availability to juvenile and
resident fishes.
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
See also AEA’s response to comment
RIVPRO-26.
11.3.1: Conduct a trophic analysis to
describe potential changes in the primary
and secondary productivity of the riverine
community following post-project
construction and operation.
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
11.3.1: Generate habitat suitability criteria
(HSC) for Susitna River benthic
macroinvertebrate and algal habitats to
predict potential change in these habitats
downstream of proposed dam site.
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
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USFWS | Study Request No. 11: River Productivity Study
Requested Study Objectives RSP Equivalent AEA Explanation
11.3.1: Characterize the benthic
macroinvertebrate compositions in the
diets of representative fish species in
relationship to their source (benthic or drift
component).
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
11.3.1: Evaluate the feasibility of reference
sites on the Talkeetna and Chulitna Rivers
to monitor baseline productivity, pre-and
post-construction.
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
11.3.1: Characterize organic matter
resources (e.g., available for
macroinvertebrate consumers)including
course particulate organic matter, fine
particulate organic matter, and suspended
organic matter in the lower, middle, and
upper Susitna River.
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
See also AEA’s response to comment
RIVPRO-26.
11.3.1: Estimate benthic macroinvertebrate
colonization rates in the middle and lower
reaches to monitor baseline conditions and
evaluate future changes to productivity in
the Susitna River.
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
Study Methodologies
Requested Study Methodologies RSP Equivalent AEA Explanation
11.3.6: Review and summarize relevant
literature, including 1980s Susitna River
data.
Section 9.8.4.1.USFWS Study Request methodology
substantially incorporated into study plan.
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USFWS | Study Request No. 11: River Productivity Study
Requested Study Methodologies RSP Equivalent AEA Explanation
11.3.6: Review and summarize the
potential effects of dams and hydropower
operations, with an emphasis on
comparably large hydroelectric projects in
cold-weather climates
Section 9.8.4.1.USFWS Study Request methodology
substantially incorporated into study plan.
11.3.6: Sampling sites will be located in
multiple locations above and below the
proposed dam site (RM 184).
Section 9.8.4. Specific details regarding
site locations, timing, sampling devices,
processing, and analyses will be dependent
upon the results of 2012 data collection
efforts.
USFWS Study Request methodology
substantially incorporated into study plan.
11.3.6: Sampling collections will be
conducted in a variety of habitats (e.g.,
riffles and large woody debris) within
mainstem, tributary confluences, side
channels, and sloughs.
Section 9.8.4.2.1. USFWS Study Request methodology
substantially incorporated into study plan.
11.3.6: Sampling will be stratified by reach
and mainstem habitat type defined in the
project specific habitat classification
scheme.
Section 9.8.4.2.1.USFWS Study Request methodology
substantially incorporated into study plan.
11.3.6: Sampling will occur in all study
years in all seasons to capture seasonal
community structure and productivity.
Section 9.8.4.2.1.USFWS Study Request methodology
substantially incorporated into study plan.
11.3.6: Efforts will be made to locate
sampling sites at transects established by
the instream flow team, in an attempt to
correlate with additional environmental
data (flow, substrates,temperature, water
quality, riparian habitat, etc.) for statistical
analys es, and HSC development.
Section 9.8.4.2.1: All stations established
within the Middle River Segment will be
located at Focus Areas established by the
Instream Flow Study (Section 8.5.4.2.1.1.),
in an attempt to correlate
macroinvertebrate data with additional
environmental data (flow, substrates,
temperature, water quality, riparian habitat,
etc.) for statistical analyses, and HSC/HSI
development.
USFWS Study Request methodology
substantially incorporated into study plan.
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22
USFWS | Study Request No. 11: River Productivity Study
Requested Study Methodologies RSP Equivalent AEA Explanation
11.3.6: Measurements of depth, mean
water column velocity, and substrate
composition will be taken concurrently
with benthic macroinvertebrate sampling at
each sample location for use in HSC
development in the instream flow studies.
Section 9.8.4.6: describing the method for
generating HSC for Susitna
macroinvertebrate and algal habitats.
USFWS Study Request methodology
substantially incorporated into study plan.
11.3.6: Investigate the ability of the river
water quality model (Water Quality
Modeling Study) to predict changes in
primary productivity in the Susitna River
with changes in turbidity and temperature.
Section 9.8.4.5.USFWS Study Request methodology
substantially incorporated into study plan.
11.3.6: Target fish species will be
determined by consultation and
coordination with fish distribution and
abundance study teams (Fish Distribution
and Abundance in the Middle and Lower
Susitna River Study, Fish Distribution and
Abundance in the Upper Susitna River
Study, and/or Salmon Escapement Study
teams).
Section 9.8.4.5.1.USFWS Study Request methodology
substantially incorporated into study plan.
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32
USFWS | Study Request Enclosure No. 13: Early Life History and Juvenile Fish
Distribution and Abundance in the Susitna River
USFWS Study Request Enclosure No. 13:
Early Life History and Juvenile Fish Distribution and Abundance in the Susitna River
Study Objectives
Requested Study Objectives RSP Equivalent AEA Explanation
13.3.1: Determine the seasonal
distribution, relative abundance (as
determined by CPUE, fish density, and
counts), and fish-habitat associations of
juvenile anadromous and juvenile resident
fish species in the mainstem Susitna River
(side channel, slough, backwater,and
tributary confluence habitats.
Sections 9.5.1 and 9.6.1.USFWS Study Request objective
substantially incorporated into study plan.
13.3.1: Describe the seasonal movements
and migratory patterns of juvenile
anadromous and resident fish species
among mainstem habitats and between
tributaries and mainstem habitats with
emphasis on identifying foraging and
overwintering habitats.
Sections 9.5.1 and 9.6.1.USFWS Study Request objective
substantially incorporated into study plan.
13.3.1: Document the timing of
downstream movement of all juvenile fish
species and outmigration for anadromous
salmon.
Sections 9.5.1 and 9.6.1.USFWS Study Request objective
substantially incorporated into study plan.
13.3.1: Document the age structure,
growth, and condition of juvenile
anadromous and juvenile resident fish by
season.
Sections 9.5.1 and 9.6.1.USFWS Study Request objective
substantially incorporated into study plan.
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33
USFWS | Study Request Enclosure No. 13: Early Life History and Juvenile Fish
Distribution and Abundance in the Susitna River
Requested Study Objectives RSP Equivalent AEA Explanation
13.3.1: Collect and analyze tissue samples
from juvenile salmon and opportunistically
from all resident and non-salmon
anadromous fish to support the Genetic
Analysis study.
Sections 9.5.1, 9.6.1 and 9.14.USFWS Study Request objective
substantially incorporated into study plan.
13.3.1: Collect and provide the Instream
Flow study with habitat suitability criteria
(HSC) data to support analysis of potential
project impacts.
Section 8.5.1.2.USFWS Study Request objective
substantially incorporated into study plan.
13.3.1: Evaluate salmon incubation
(embryo development, hatching success,
and emergence times) and associated water
quality conditions (e.g., temperature, DO,
pH) at existing spawning habitats (slough,
side channel, tributary, and mainstem) in
areas with and without groundwater
upwelling in the middle and lower reaches
of the Susitna River.
Sections 8.5.1.2 and 9.6.1,except AEA’s
study plan does not include evaluation of
embryo development and hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
13.3.1: Evaluate the potential for stranding
of juvenile fish and stranding mortality by
season under proposed operational
conditions.
Sections 8.5.4.5.1.2.2, 8.5.4.6.1.1.4 and
8.5.4.6.1.6.1.
USFWS Study Request objective
substantially incorporated into study plan.
13.3.1: Measure intragravel water
temperature in spawning habitats and
winter juvenile fish habitats at different
surface elevations and different depths to
determine the potential for freezing of
redds, freezing of juvenile fish, and their
habitats.
Section 8.5.1.2.USFWS Study Request objective
substantially incorporated into study plan.
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34
USFWS | Study Request Enclosure No. 13: Early Life History and Juvenile Fish
Distribution and Abundance in the Susitna River
Study Methodologies
Requested Study Methodologies RSP Equivalent AEA Explanation
13.3.5: Collect data using standard
sampling techniques (e.g., electrofishing,
snorkeling,minnow trapping, and seining)
by season. For winter sampling may also
use PIT tag arrays, video systems, or both.
Sections 9.5.1, 9.5.4.3.1, 9.5.4.4 and
9.6.4.3.1.
USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Estimate and compare the relative
abundance of juvenile salmon within and
across mainstem habitats by season.
Sections 9.5.4.3.1 and 9.6.4.3.1: Relative
abundance surveys will include seasonal
multi-pass sampling events during the ice-
free seasons. As mentioned above,
methods will be selected based on species,
life stage, and water conditions.
Section 9.7.4.5: A comparison will be
made of results from 2012–2014 studies to
the historical results that characterized the
relative abundance, locations of spawning
and holding salmon, and use of mainstem,
side channel, slough, and tributary habitat
types by adult salmon.
USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Determine the seasonal use and
movement patterns of marked/tagged
juvenile fish between mainstem habitats
strategically selected based on an
appropriate sampling strategy (i.e.,
systematic, random, or stratified random
design).
Sections 9.5.4.1 and 9.6.4.1.USFWS Study Request methodology
substantially incorporated into study plan.
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35
USFWS | Study Request Enclosure No. 13: Early Life History and Juvenile Fish
Distribution and Abundance in the Susitna River
Requested Study Methodologies RSP Equivalent AEA Explanation
13.3.5: Estimate juvenile salmon
production of the Susitna River at selected
sites.
No equivalent methodology in RSP.AEA will not be collecting data to generate
population estimates necessary for
determining salmon production. At
request of USFWS, AEA agreed to
eliminate population estimates in order to
expand the number of sampling sites by
collecting only relative abundance and
present-absence data. See AEA’s response
to comment FDAML-54, RSP Appendix 1.
13.3.5: Determine the relative timing,
distribution, and abundance of juvenile
salmon in mainstem habitats and compare
to historical data.
Sections 9.5.4.3.1 and 9.6.4.3.1.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Determine the distribution, and
abundance of juvenile salmon in mainstem
and tributary habitats upstream of the
proposed Watana Dam site during open
water (May through October).
Sections 9.5.4.3.1.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Use systematic scheme for
sampling across habitat types by season
and randomize selection of habitat units to
sample.
Sections 9.5.4.1 and 9.6.4.1.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Build upon and use, as appropriate,
the 1980s data applicable to non-salmon
anadromous, resident, and invasive fish
species.
Sections 9.5.4.3 and 9.6.4.3.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Establish a seasonal sampling
design that includes turbid and clearwater
sampling for these species (as appropriate).
Section 9.6.4.2.AEA is not specifically targeting turbid
and clear water, but AEA anticipates that,
by monthly sampling side-channel and
sloughs, AEA will be sampling under
turbid and clear water conditions.
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36
USFWS | Study Request Enclosure No. 13: Early Life History and Juvenile Fish
Distribution and Abundance in the Susitna River
Requested Study Methodologies RSP Equivalent AEA Explanation
13.3.5: Sample fish species using
appropriate methods for the habitat and
season (electrofishing, snorkeling, seining,
minnow trapping) in the main channel,
side channels,sloughs,and tributary
mouths.
Sections 9.5.4.4 and 9.6.4.4.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Develop life stage specific
periodicity information for the middle and
lower reach in support of the Instream
Flow Study.
Sections 9.5.4.3 and 9.6.4.3: Preparation of
periodicity charts for each species within
the study area (timing of adult migration,
holding, and spawning; timing of
incubation, rearing, and out-migration).
USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Collect additional data to support
efforts to determine the timing,
distribution, and relative abundance of
eulachon in the lower reach of the Susitna
River.
Section 9.16.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Coordinate with other Project
studies as appropriate (e.g., fish and
physical characteristics of the river).
Sections 9.5.7 and 9.6.7.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Coordinate with the Synthesis of
Existing Fish Population Data Study to
summarize and obtain the 1980s study data
applicable to juvenile salmon, non-salmon
anadromous,resident and invasive fish
species.
Sections 9.5.4.3 and 9.6.4.3.USFWS Study Request methodology
substantially incorporated into study plan.
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37
USFWS | Study Request Enclosure No. 13: Early Life History and Juvenile Fish
Distribution and Abundance in the Susitna River
Requested Study Methodologies RSP Equivalent AEA Explanation
13.3.5: Use PIT tag antenna arrays near the
mouths of select tributaries and sloughs or
other mainstem habitats to determine
seasonal habitat utilization (mainstem vs.
tributary/slough) and movements of
targeted fish species in the reach between
the Deshka River and the Watana Dam
site.
Sections 9.5.4.4.12 and 9.6.4.4.12.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Collect, radio tag, and track fish
from selected species. Tag sizes will be
chosen to maximize tag life within the
constraints of the study fish size. Tracking
duration will be determined based on the
anticipated life span of the tags chosen.
Sections 9.5.4.4.12 and 9.6.4.4.12.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Operate PIT arrays at strategic side
channels, sloughs, or other mainstem
habitats, and the confluence of tributaries
to allow for tracking of individual fish
among mainstem habitats.
Sections 9.5.4.4.12 and 9.6.4.4.12.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Use data from inclined plane,
rotary screw traps, or both, in the
mainstem to determine the timing of all
salmon species emigrating from the upper
reach (i.e., Watana Dam site)and from the
middle reach of the Susitna River.
Sections 9.5.4.4.10 and 9.6.4.4.10.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Collect fish length and weight data
during seasonal fish surveys in Objectives
1 and 3.
Sections 9.5.4 and 9.6.4.USFWS Study Request methodology
substantially incorporated into study plan.
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38
USFWS | Study Request Enclosure No. 13: Early Life History and Juvenile Fish
Distribution and Abundance in the Susitna River
Requested Study Methodologies RSP Equivalent AEA Explanation
13.3.5: Collect fish length and weight data
from fish recaptured with PIT tags during
seasonal fish surveys in individual to
determine individual fish growth rates by
season.
Section 9.5.4.4.12 and 9.6.4.4.12.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Use fish length and weight data to
calculate fish condition by season and
possibly habitat (e.g., in areas with and
without groundwater upwelling).
Sections 9.5.4.3.1, 9.5.4.3.3, 9.6.4.3.1 and
9.5.4.3.3.
USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Coordinate with the Genetic
Analysis study to identify the appropriate
target species and genetic sampling
protocols to opportunistically collect
genetic tissue samples from resident
species.
Sections 9.5.4.3.7 and 9.6.4.3.7: In support
of the Genetic Baseline Study for Selected
Fish Species (Section 9.14), fish tissues
will be collected opportunistically in
conjunction with all fish capture events.
USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Coordinate with the Genetic Study
to identify the appropriate target species,
sampling locations, number of samples per
species, and genetic sampling protocols to
collect sufficient genetic samples from
juvenile salmon.
Sections 9.5.4.3.7 and 9.6.4.3.7.USFWS Study Request methodology
substantially incorporated into study plan.
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39
USFWS | Study Request Enclosure No. 13: Early Life History and Juvenile Fish
Distribution and Abundance in the Susitna River
Requested Study Methodologies RSP Equivalent AEA Explanation
13.3.5: Systematic surveys will include
collection of data for input parameters to
IFIM analyses.Specifically, data will
include species, length, location in the
water column (distance from the bottom),
substrate use classification, proximity/
affinity to habitat structure/cover features
(e.g., boulder, undercut bank, overhanging
vegetation, large woody debris),water
depth, mean column velocity, water
temperature, and relevant comments
pertaining to cover associations and/or
behavioral characteristics of the fish
observed.
Section 8.5.1.2.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Use modified Whitlock-Vibert
boxes or similar methodology to monitor
egg development,hatching success, and
emergence times in areas with and without
groundwater upwelling. Consider using
approved hatchery fish source or fish
spawned in the field.
Sections 8.5.4.5.1.1.5 and 9.6.1, except
AEA’s study plan does not include
evaluation of embryo development and
hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
13.3.5: Use siphons to monitor egg
development and emergence in naturally
occurring salmon spawning areas.
Sections 8.5.4.5.1.1.5 and 9.6.1, except
AEA’s study plan does not include
evaluation of embryo development and
hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
13.3.5: Assess egg development and
survival of embryos: one potential method
could include creating artificial redds and
burying egg tubes in known spawning
habitats.
Sections 8.5.4.5.1.1.5 and 9.6.1, except
AEA’s study plan does not include
evaluation of embryo development and
hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
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40
USFWS | Study Request Enclosure No. 13: Early Life History and Juvenile Fish
Distribution and Abundance in the Susitna River
Requested Study Methodologies RSP Equivalent AEA Explanation
13.3.5: Monitor water quality parameters
such as temperature and dissolved oxygen
in spawning gravels and redds.
Sections 8.5.4.5.1.1.5 and 8.5.4.5.1.2.1.USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Refine and use methods similar to
those used in the 1980s, or use other
methodologies,to evaluate embryo
development, hatching success, and
emergence times.
Sections 8.5.4.5.1.1.5 and 9.6.1, except
AEA’s study plan does not include
evaluation of embryo development and
hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
13.3.5: Use or consider other potential
methods to determine or estimate fry
emergence times (e.g., incline plane traps,
fry emergence traps), as appropriate.
Sections 8.5.4.5.1.1.5, 9.6.1, and 9.6.4.3.3,
except AEA’s study plan does not include
evaluation of embryo development and
hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
13.3.5: Monitor range and peak of
emergence times and by time of day.
No equivalent methodology in RSP.The method is not useful in assessing
potential Project effects because the scale
of this method is too fine and is influenced
by variable site-specific conditions.
13.3.5: Identify habitats occupied by
juvenile fish (<50 mm in length) using the
distribution and abundance information
obtained from Objectives 1 and 2.
Section 9.6.4.3.3.
Section 9.5.4.1 and 9.6.4.1: Fish
distribution sampling will occur at Focus
Areas and at representative habitat units to
identify seasonal timing, size, and
distribution among habitat types for fish
(particularly < 50 mm).
USFWS Study Request methodology
substantially incorporated into study plan.
13.3.5: Monitor juvenile fish activity by
season and time of day to determine
periods of activity and inactivity (e.g.,
when using cover, interstices of gravel).
Section 9.6.4.3.3.USFWS Study Request methodology
substantially incorporated into study plan.
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42
USFWS | Study Request Enclosure No. 14: Adult and juvenile non-salmon anadromous, resident
and invasive fish studies in the Susitna River basin (RM 0 -RM 233).
USFWS Study Request Enclosure No. 14:
Adult and Juvenile Non-Salmon Anadromous, Resident and Invasive Fish Studies in the Susitna River Basin (RM 0 -RM 233)
Study Objectives
Requested Study Objectives RSP Equivalent AEA Explanation
14.3.1: Characterize the seasonal (spring,
summer, fall, winter) distribution, relative
abundance,and habitat utilization in the
Susitna River mainstem (RM 0-RM 233)
for all life stages of non-salmon
anadromous, resident, and invasive fish
species. [Documenting both hierarchal
nested habitat type and use-type as
described in the resource agency Instream
Flow Study and Habitat Utilization Study
Request].
Section 9.5.1 and 9.6.3, except limited to
upper reach of the Lower River, Middle
River, and Upper River segments.
Section 9.16.
See AEA’s response to comment FDAML-
01.
14.3.1: Characterize the seasonal (spring,
summer, fall and winter) movement
patterns of all subject fish species and life
stages as they relate to foraging, spawning,
rearing and overwintering habitats. The
characterization of seasonal movements
includes run timing (immigration and
emigration) and extent (periodicity) of
non-salmon anadromous species in the
Susitna River (RM 0-RM 233) and
movement into and out of tributary
streams.[Interface with resource agency
Instream Flow and Habitat Utilization
Study Request hierarchal nested habitat
types and habitat mapping].
Section 9.5.1 and 9.6.1,except limited to
upper reach of the Lower River, Middle
River, and Upper River segments.
See AEA’s response to comment FDAML-
01.
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43
USFWS | Study Request Enclosure No. 14: Adult and juvenile non-salmon anadromous, resident
and invasive fish studies in the Susitna River basin (RM 0 -RM 233).
Requested Study Objectives RSP Equivalent AEA Explanation
14.3.1: Characterize the flow-related or
synchronized life history strategies
(migration,movement, spawning, rearing,
hatching, emergence) of non-salmon
anadromous,resident and invasive species,
and their biological behavioral response
(e.g., potential for false attraction, delayed
migration or increased holding time,
synchrony of spawning,relative hatching
and emergence timing) to Project-affected
flow alterations (flow,temperature,
habitat, water quality).
Sections 8.5, 9.5.1 and 9.6.1 characterize
life history strategy and habitat use of all
target species.
See AEA’s response to comment FISH-06.
14.3.1: Synthesize existing resource data,
results and information from 1980’s
Susitna Hydroelectric studies, and other
relevant literature to determine
applicability and utility of results and
information to the currently proposed
project.
Sections 9.5.1 and 9.6.1.USFWS Study Request objective
substantially incorporated into study plan.
14.3.1:Collect tissue samples from all
resident and non-salmon anadromous fish
species for genetic population structure
database and future stock identification
analysis. This is particularly important for
salmon species, anadromous lamprey, and
Bering cisco of the Susitna River drainage.
Sections 9.5.1 and 9.6.1.USFWS Study Request objective
substantially incorporated into study plan.
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44
USFWS | Study Request Enclosure No. 14: Adult and juvenile non-salmon anadromous, resident
and invasive fish studies in the Susitna River basin (RM 0 -RM 233).
Requested Study Objectives RSP Equivalent AEA Explanation
14.3.1:Characterize trophic interactions
using seasonal diets (stomach content
analysis) of all age classes of non-salmon
anadromous, resident and invasive fish
species. [Interface with the productivity
study, riparian, and instream flow study
requests]
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
14.3.1:Quantify the relative contribution
(biomass) of marine-derived nutrients to
the ecology of the Susitna River from adult
returns of non-salmon anadromous fish
species (e. g.,Pacific and Arctic lamprey,
eulachon, Bering cisco).
Section 9.8.1.USFWS Study Request objective
substantially incorporated into study plan.
Study Methodologies
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Fish distribution surveys should use
the hierarchal nesting of habitats described
in the resource agency’s Instream Flow
and Habitat Utilization Study Request to
document and describe habitat types.
Sections 9.5.4.1 and 9.6.4.1. USFWS Study Request methodology
substantially incorporated into study plan.
1.3.6: The distribution and movement
patterns of these fish should be
characterized using remote tagging
techniques, such as telemetry and pit-
tagging.
Sections 9.5.4.4.12 and 9.6.4.4.12. USFWS Study Request methodology
substantially incorporated into study plan.
1.3.6: Relative abundances should be
developed using weirs, mark-recapture,
netting or trapping in combination with
scientifically sound statistical analysis.
Sections 9.5.4.4, 9.6.4.4 and 9.7.4.USFWS Study Request methodology
substantially incorporated into study plan.
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45
USFWS | Study Request Enclosure No. 14: Adult and juvenile non-salmon anadromous, resident
and invasive fish studies in the Susitna River basin (RM 0 -RM 233).
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: A minimum of two years of baseline
assessment of gear types, including that for
winter sampling is necessary before valid
fish distribution or habitat use data can be
collected.
No equivalent methodology in RSP.A minimum of two years of baseline
assessment of gear types is not needed to
meet the goals and objectives of the study
plan. See Sections 9.5.5 and 9.6.5.
1.3.6: Electro-fishing, trap netting, gill
netting, and telemetry studies are widely
accepted methods for sampling and
observing behavior and habitat selection of
fish populations in stream, river and
reservoir habitats.
Sections 9.5.4.4 and 9.6.4.4. USFWS Study Request methodology
substantially incorporated into study plan.
1.3.6: Seasonal representative stomach
content samples of all species should be
collected using current scientific
methodologies and protocols for a
quantitative analysis.
Section 9.5.4.4.11 and 9.6.4.4.14: A total
of eight fish per target species/age class
per sampling site collection will be
sampled for fish stomach contents, using
non-lethal methods (described in Section
9.8.4.7).
Section 9.8.4.7: Characterize the
invertebrate compositions in the diets of
representative fish species in relationship
to their source (benthic or drift
component).
USFWS Study Request methodology
substantially incorporated into study plan.
1.3.6: All data generated during this study
will be incorporated into a geospatially-
referenced relational database.
Generally incorporated into all applicable
studies.
USFWS Study Request methodology
substantially incorporated into study plan.
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47
USFWS | Study Request Enclosure No. 15: Adult Salmon Distribution, Abundance,
Habitat Utilization and Escapement in the Susitna River
Requested Study Objectives RSP Equivalent AEA Explanation
15.3.1: Estimate escapement of adult
salmon spawning by mainstem reaches and
tributaries.
Section 9.7.1.2: Estimate the system-wide
Chinook salmon escapement to the entire
Susitna River, the coho salmon escapement
to the Susitna River above the its
confluence with the Yentna River, and the
distribution of Chinook, coho, and pink
salmon among tributaries of the Susitna
River (upstream of Yentna River
confluence) in 2013 and 2014.
USFWS Study Request objective
substantially incorporated into study plan.
15.3.1: Collect tissue samples to support
the Genetic Analys is Study.
Section 9.7.1.2: Collect tissue samples to
support the Fish Genetic Baseline Study
(Section 9.14).
Sections 9.5.1, 9.5.4.3.7 and 9.6.1: Collect
tissue samples from juvenile salmon and
opportunistically from all resident and
non-salmon anadromous fish to support the
Genetic Baseline Study (Section 9.14,
which includes a dedicated and focused
sampling effort to collect salmon and
resident fish tissues).
USFWS Study Request objective
substantially incorporated into study plan.
15.3.1: Determine system-wide Susitna
River escapement and run apportionment.
Section 9.7.1.2, by developing Chinook
and coho salmon system and river-wide
escapement estimates in 2013 and 2014.
These will be added to and build upon the
system-wide estimates developed in recent
years for all other species except pink
salmon.
USFWS Study Request objective
substantially incorporated into study plan.
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51
USFWS | Study Request Enclosure No. 15: Adult Salmon Distribution, Abundance,
Habitat Utilization and Escapement in the Susitna River
Requested Study Methodologies RSP Equivalent AEA Explanation
15.3.5: Identify potential barriers to
salmon spawning habitats by species.
2012 Salmon Escapement and Upper
Susitna River Fish Distribution and Habitat
Study efforts began to address this
objective (Sections 9.5.6 and 9.7.4).
Additional data will be collected during
2013 and 2014 pursuant to Sections 9.12.1
and 9.9.4.
USFWS Study Request methodology
substantially incorporated into study plan.
15.3.5: Determine flows needed for salmon
access to tributaries and mainstem
spawning habitats (e.g., sloughs and side
channels).
Sections 9.12.4 and 8.5.4.6.1.2.3.USFWS Study Request methodology
substantially incorporated into study plan.
15.3.5: Estimate the available spawning
habitat for all salmon species (Chinook,
coho, chum,pink, and sockeye) in the
mainstem Susitna River in all reaches.
No equivalent methodology in RSP.Although AEA is not quantifying available
habitat, AEA will, through instream flow
modeling, quantify flow-habitat
relationships for spawning habitat and will
address potential project effects to that
habitat. See Section 8.5.
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ATTACHMENT 2
CROSSWALK TABLE BETWEEN
NATIONAL MARINE FISHERIES SERVICE STUDY REQUESTS
(MAY 31, 2012)
AND
ALASKA ENERGY AUTHORITY REVISED STUDY PLAN
(DECEMBER 14, 2012)
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1
NMFS | Study Request Enclosure No. 3:Fish Passage Study Request
CROSSWALK TABLE BETWEEN
NATIONAL MARINE FISHERIES SERVICE STUDY REQUESTS (MAY 31, 2012)
AND
ALASKA ENERGY AUTHORITY REVISED STUDY PLAN (DECEMBER 14, 2012)
NMFS Study Request Enclosure No. 3:
Fish Passage Study Request
Study Objectives
Requested Study Objectives RSP Equivalent AEA Explanation
1.3.1: Determine the distribution of adult
and juvenile Chinook salmon and relative
abundance of juvenile Chinook salmon in
the Susitna River and its tributaries above
Devils Canyon for 2012.
2012 Salmon Escapement and Upper
Susitna River Fish Distribution and Habitat
Study efforts began to address this
objective (Sections 9.5.6 and 9.7.4).
Additional data will be collected during
2013 and 2014 pursuant to Sections 9.5.1,
9.6.1 and 9.7.1.2.
NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Characterize aquatic habitat in the
Susitna River and its tributaries/lakes from
Devils Canyon upstream to and including
the Oshetna River and determine its
suitability for Chinook salmon.
Section 9.9.NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Determine the fish species
composition and relative abundance of all
fish species within the reservoir inundation
zone in 2012.
2012 Salmon Escapement and Upper
Susitna River Fish Distribution and Habitat
Study efforts began to address this
objective (Sections 9.5.6 and 9.7.4).
Additional data will be collected during
2013 and 2014 pursuant to Section 9.5.1.
NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Characterize the type and amount of
aquatic habitat within the reservoir
inundation zone.
Section 9.9.2.NMFS Study Request objective
substantially incorporated into study plan.
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NMFS | Study Request Enclosure No. 3:Fish Passage Study Request
Requested Study Objectives RSP Equivalent AEA Explanation
1.3.1: Identify the locations of potential
fish barriers in tributaries between Devils
Canyon and the Oshetna River.
2012 Salmon Escapement and Upper
Susitna River Fish Distribution and Habitat
Study efforts began to address this
objective (Sections 9.5.6 and 9.7.4).
Additional data will be collected during
2013 and 2014 pursuant to Section 9.12.1.
NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Collect genetic samples of Chinook
salmon.
Section 9.14.1: Develop a repository of
genetic samples for fish species captured
within the Susitna River drainage, with an
emphasis on those species found in the
Middle and Upper Susitna River.
NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Assist in the development of the
2013-2014 study plans for resident and
anadromous fish upstream of Devils
Canyon.
No equivalent objective in RSP.AEA has involved NMFS and other
licensing participants in the development
of study plans.
1.3.2:Maintaining native and natural
aquatic communities for their intrinsic and
ecological value and their benefits to
people. This includes habitat protection
and maintenance to ensure the health and
survival of all species and natural
communities.
No equivalent objective in RSP.While not an objective of AEA’s study
plan, this type of resource management
objective will be considered when
developing proposed protection,
mitigation, and enhancement measures
(PM&E measures). See cover letter for
further explanation.
1.3.2: Maintaining stream flow regimes
sufficient to sustain native riparian and
aquatic habitats in the project-affected
stream reaches.
No equivalent objective in RSP.While not an objective of AEA’s study
plan, this type of resource management
objective will be considered when
developing proposed PM&E measures.
See cover letter for further explanation.
1.3.2: Maintaining the diversified use of
fish and wildlife including commercial,
recreational, scientific and educational
purposes.
No equivalent objective in RSP.While not an objective of AEA’s study
plan, this type of resource management
objective will be considered when
developing proposed PM&E measures.
See cover letter for further explanation.
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5
NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
NMFS Study Request Enclosure No. 4:
Early Life History and Juvenile Fish Distribution and Abundance in the Susitna River Study Request
Study Objectives
Requested Study Objectives RSP Equivalent AEA Explanation
1.3.1: Determine the seasonal distribution,
relative abundance (as determined by
CPUE, fish density, and counts), and fish-
habitat associations of juvenile
anadromous and resident juvenile fish
species in the mainstem Susitna River (side
channel, slough, backwater, and tributary
confluence habitats.
Section 9.6.1.NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Describe the seasonal movements of
juvenile anadromous and resident juvenile
fish species among mainstem habitats and
between tributaries and mainstem habitats
with emphasis on identifying foraging and
over-wintering habitats.
Sections 9.5.1 and 9.6.1.NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Document the timing of downstream
movement of all juvenile fish species, and
outmigration for anadromous salmon.
Sections 9.5.1 and 9.6.1.NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Characterize the age structure,
growth, and condition of juvenile
anadromous and juvenile resident fish by
season.
Sections 9.5.1 and 9.6.1.NMFS Study Request objective
substantially incorporated into study plan.
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NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
Requested Study Objectives RSP Equivalent AEA Explanation
1.3.1: Collect and analyz e tissue samples
from juvenile salmon and opportunistically
from all resident and non-salmon
anadromous fish to support the Genetic
Analysis study.
Sections 9.5.1, 9.6.1 and 9.14.4.1.NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Collect and provide the instream
flow study with habitat suitability criteria
(HSC) data to support analysis of potential
project impacts.
Section 8.5.1.2.NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Evaluate salmon incubation (embryo
development, hatching success, and
emergence times) and monitor associated
water quality conditions (e.g., temperature,
DO, pH) at existing spawning habitats
(slough, side channel, tributary, and
mainstem) in areas with and without
groundwater upwelling in the middle and
lower reaches of the Susitna River.
Section 8.5.2.1 and Section 9.6.1, except
that AEA’s study plan does not include
evaluation of embryo development and
hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
1.3.1: Evaluate the potential for stranding
of juvenile fish and stranding mortality by
season under proposed project operational
conditions.
Section 8.5.4.5.1.2.2, 8.5.4.6.1.1.4 and
8.5.4.6.1.6.1.
NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Measure intragravel water
temperature in spawning habitats and
winter juvenile fish habitats at different
surface elevations and different depths to
determine the potential for freezing of
redds, freezing of juvenile fish, and their
habitats.
Section 8.5.4.5.1.2.1.NMFS Study Request objective
substantially incorporated into study plan.
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NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
Requested Study Objectives RSP Equivalent AEA Explanation
1.3.2: Maintaining riparian resources,
channel conditions, and aquatic habitats.
No equivalent objective in RSP.While not an objective of AEA’s study
plan, this type of resource management
objective will be considered when
developing proposed PM&E measures.
See cover letter for further explanation.
1.3.2: Maintaining stream flow regimes
sufficient to sustain desired conditions of
native riparian, aquatic, and wetland
habitats.
No equivalent objective in RSP.While not an objective of AEA’s study
plan, this type of resource management
objective will be considered when
developing proposed PM&E measures.
See cover letter for further explanation.
1.3.2: Protecting aquatic systems to which
species are uniquely adapted.
No equivalent objective in RSP.While not an objective of AEA’s study
plan, this type of resource management
objective will be considered when
developing proposed PM&E measures.
See cover letter for further explanation.
Study Methodologies
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Collect data using standard sampling
techniques (e.g., electrofishing, snorkeling,
minnow trapping, and seining) by season.
For winter sampling may also use PIT tag
arrays, video systems, or both.
Sections 9.5.4.3.1 9.5.4.4 and 9.6.4.3.1.NMFS Study Request methodology
substantially incorporated into study plan.
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9
NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Estimate and compare the relative
abundance of juvenile salmon within and
across mainstem habitats by season.
Sections 9.5.4.3.1 and 9.6.4.3.1: Relative
abundance surveys will include seasonal
multi-pass sampling events during the ice-
free seasons. As mentioned above,
methods will be selected based on species,
life stage, and water conditions.
Section 9.7.4.5: A comparison will be
made of results from 2012–2014 studies to
the historical results that characterized the
relative abundance, locations of spawning
and holding salmon, and use of mainstem,
side channel, slough, and tributary habitat
types by adult salmon.
NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6:Determine the seasonal use and
movement patterns of marked/tagged
juvenile fish between mainstem habitats
strategically selected based on an
appropriate sampling strategy (i.e.,
systematic, random, or stratified random
design).
Sections 9.5.4.1, 9.5.4.3.2,9.6.4.1 and
9.6.4.3.2.
NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6:Estimate juvenile salmon production
of the Susitna River at selected sites.
No equivalent methodology in RSP.AEA will not be collecting data to generate
population estimates necessary for
determining salmon production. At
request of USFWS, AEA agreed to
eliminate population estimates in order
expand the number of sampling sites by
collecting only relative abundance and
present-absence data. See AEA’s response
to comment FDAML-54, RSP Appendix 1.
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NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Determine the relative timing,
distribution, and abundance of juvenile
salmon in mainstem habitats and compare
to historical data.
Sections 9.5.4.3.1 and 9.6.4.3.1.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Determine the distribution, and
abundance of juvenile salmon in mainstem
and tributary habitats upstream of the
proposed Watana Dam site during open
water (May through October).
Section 9.5.4.3.1.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Use systematic scheme for sampling
across habitat types by season and
randomize selection of habitat units to
sample.
Sections 9.5.4.1 and 9.6.4.1.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Build upon and use, as appropriate,
the 1980s data applicable to non-salmon
anadromous,resident, and invasive fish
species.
Sections 9.5.4.3 and 9.6.4.3.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Establish a seasonal sampling design
that includes turbid and clear water
sampling for these species (as appropriate).
Section 9.6.4.2.AEA is not specifically targeting turbid
and clear water, but AEA anticipates that,
by monthly sampling side-channel and
sloughs, AEA will be sampling under
turbid and clear water conditions.
1.3.6: Sample fish species using
appropriate methods for the habitat and
season (electrofishing,snorkeling, seining,
minnow trapping) in the main channel,
side channels, sloughs, and tributary
mouths.
Sections 9.5.4.4 and 9.6.4.4.NMFS Study Request methodology
substantially incorporated into study plan.
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NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Develop life stage specific
periodicity information for the middle and
lower reach in support of the Instream
Flow Study.
Sections 9.5.4.3 and 9.6.4.3: Preparation of
periodicity charts for each species within
the study area (timing of adult migration,
holding, and spawning; timing of
incubation, rearing, and out-migration).
NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Collect additional data to support
efforts to determine the timing,
distribution, and relative abundance of
eulachon in the lower reach of the Susitna
River.
Section 9.16.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Coordinate with the Synthesis of
Existing Fish Population Data Study to
summarize and obtain the 1980s study data
applicable to juvenile salmon, non-salmon
anadromous,resident and invasive fish
species.
Sections 9.5.4.3 and 9.6.4.3.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Selectively mark individual fish
collected during seasonal surveys
conducted under study Objective 1 and
Objective 4 with PIT-tags.
Sections 9.5.4.4.12 and 9.6.4.12.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Use PIT tag antenna arrays near the
mouths of select tributaries and sloughs or
other mainstem habitats to determine
seasonal habitat utilization (mainstem vs.
tributary/slough) and movements of
targeted fish species in the reach between
the Deshka River and the Watana Dam
site.
Sections 9.5.4.4.12 and 9.6.4.12.NMFS Study Request methodology
substantially incorporated into study plan.
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NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Coordinate with salmon escapement
and fish survey teams to retrieve data from
PIT-tag detections and from fish wheel
operations related to non-salmon
anadromous, resident,and invasive species
collected during their studies.
Sections 9.5.7 and 9.6.7.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Collect, radio tag, and track fish
from selected species. Tag sizes will be
chosen to maximize tag life within the
constraints of the study fish size. Tracking
duration will be determined based on the
anticipated life span of the tags chosen.
Sections 9.5.4.4.12 and 9.6.4.4.12.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Use relative abundance and marking
data from Objectives 1 and 2 to determine
patterns of movement among mainstem
habitats by season.
Sections 9.5.4.4.12 and 9.6.4.4.12.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Operate PIT arrays at strategic side
channels, sloughs, or other mainstem
habitats, and the confluence of tributaries
to allow for tracking of individual fish
among mainstem habitats.
Sections 9.5.4.4.12 and 9.6.4.4.12.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Use data from inclined plane, rotary
screw traps, or both, in the mainstem to
determine the timing of all salmon species
emigrating from the upper reach (i.e.,
Watana Dam site)and from the middle
reach of the Susitna River.
Sections 9.5.4.4.10 and 9.6.4.4.10.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Collect fish length and weight data
during seasonal fish surveys in Objectives
1 and 3.
Sections 9.5.4 and 9.6.4.NMFS Study Request methodology
substantially incorporated into study plan.
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13
NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Collect fish length and weight data
from fish recaptured with PIT tags during
seasonal fish surveys in individual to
determine individual fish growth rates by
season.
Sections 9.5.4.4.12 and 9.6.4.4.12.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Use fish length and weight data to
calculate fish condition by season and
possibly habitat (e.g., in areas with and
without groundwater upwelling).
Sections 9.5.4.3.1,9.5.4.3.3, 9.6.4.3.1 and
9.5.4.3.3.
NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Coordinate with the Genetic
Analysis study to identify the appropriate
target species and genetic sampling
protocols to opportunistically collect
genetic tissue samples from resident
species.
Sections 9.5.4.3.7 and 9.6.4.3.7: In support
of the Genetic Baseline Study for Selected
Fish Species (Section 9.14), fish tissues
will be collected opportunistically in
conjunction with all fish capture events.
NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Coordinate with the Genetic Study
to identify the appropriate target species,
sampling locations, number of samples per
species, and genetic sampling protocols to
collect sufficient genetic samples from
juvenile salmon.
Sections 9.5.4.3.7 and 9.6.4.3.7.NMFS Study Request methodology
substantially incorporated into study plan.
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14
NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Systematic surveys will include
collection of data for input parameters to
IFIM analyses.Specifically, data will
include species, length, location in the
water column (distance from the bottom),
substrate use classification, proximity/
affinity to habitat structure/cover features
(e.g., boulder, undercut bank, overhanging
vegetation, large woody debris),water
depth, mean column velocity, water
temperature, and relevant comments
pertaining to cover associations and/or
behavioral characteristics of the fish
observed.
Section 8.5.1.2.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Use modified Whitlock-Vibert boxes
or similar methodology to monitor egg
development, hatching success, and
emergence times in areas with and without
groundwater upwelling. Consider using
approved hatchery fish source or fish
spawned in the field.
Sections 8.5.4.5.1.1.5 and 9.6.1, except
that AEA’s study plan does not include
evaluation of embryo development and
hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
1.3.6: Use siphons to monitor egg
development and emergence in naturally
occurring salmon spawning areas.
Sections 8.5.4.5.1.1.5 and 9.6.1, except
that AEA’s study plan does not include
evaluation of embryo development and
hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
1.3.6: Assess egg development and
survival of embryos: one potential method
could include creating artificial redds and
burying egg tubes in known spawning
habitats.
Sections 8.5.4.5.1.1.5 and 9.6.1, except
that AEA’s study plan does not include
evaluation of embryo development and
hatching success.
See AEA’s response to comment FDAML-
87, RSP Appendix 1.
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NMFS | Study Request Enclosure No. 4:Early Life History and Juvenile Fish Distribution
and Abundance in the Susitna River Study Request
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Monitor water quality parameters
such as temperature and dissolved oxygen
in spawning gravels and redds.
Sections 8.5.4.5.1.1.5 and 8.5.4.5.1.2.1.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Refine and use methods similar to
those used in the 1980s, or use other
methodologies, to evaluate embryo
development, hatching success, and
emergence times.
Sections 8.5.4.5.1.1.5 and 9.6.1, except
that AEA’s study plan does not include
evaluation of embryo development and
hatching success.
NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Use or consider other potential
methods to determine or estimate fry
emergence times (e.g., incline plane traps,
fry emergence traps), as appropriate.
Sections 8.5.4.5.1.1.5,9.6.1,and 9.6.4.3.3,
except that AEA’s study plan does not
include evaluation of embryo development
and hatching success.
NMFS Study Request methodology
substantially incorporated.
1.3.6: Monitor range and peak of
emergence times and by time of day.
No equivalent methodology in RSP.AEA does not believe this methodology
would be useful in assessing potential
Project effects because the scale of this
method is too fine and is influenced by
variable site-specific conditions.
1.3.6: Identify habitats occupied by
juvenile fish (<50 mm in length) using the
distribution and abundance information
obtained from Objectives 1 and 2.
Section 9.6.4.3.3.
Section 9.5.4.1: Fish distribution sampling
will occur at Focus Areas and at
representative habitat units to identify
seasonal timing, size, and distribution
among habitat types for fish (particularly <
50 mm).
NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Monitor juvenile fish activity by
season and time of day to determine
periods of activity and inactivity (e.g.,
when using cover, interstices of gravel).
Section 9.6.4.3.3.NMFS Study Request methodology
substantially incorporated into study plan.
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18
NMFS | Study Request Enclosure No. 5:Adult Salmon Distribution, Abundance, Habitat Utilization
and Escapement in the Susitna River Study Request
Requested Study Objectives RSP Equivalent AEA Explanation
1.3.1: Compare historical and current data
on run timing, distribution, relative
abundance, and specific locations of
spawning and holding salmon to determine
the persistence (if any) of habitat use and
the utility of data collected during the early
1980s.
Section 9.7.1.2.NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Estimate escapement of adult
salmon spawning by mainstem reaches and
tributaries.
Section 9.7.1.2: Estimate the system-wide
Chinook salmon escapement to the entire
Susitna River, the coho salmon escapement
to the Susitna River above the its
confluence with the Yentna River, and the
distribution of Chinook, coho, and pink
salmon among tributaries of the Susitna
River (upstream of Yentna River
confluence) in 2013 and 2014.
NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Collect and analyz e tissue samples
of all salmon species as described by
ADF&G with emphasis on Chinook
salmon, to support the Genetic Analysis
Study.
Section 9.7.1.2: Collect tissue samples to
support the Fish Genetic Baseline Study
(Section 9.14).
Sections 9.5.1, 9.5.4.3.7, and 9.6.1: Collect
tissue samples from juvenile salmon and
opportunistically from all resident and
non-salmon anadromous fish to support the
Genetic Baseline Study (Section 9.14,
which includes a dedicated and focused
sampling effort to collect salmon and
resident fish tissues).
NMFS Study Request objective
substantially incorporated into study plan.
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NMFS | Study Request Enclosure No. 5:Adult Salmon Distribution, Abundance, Habitat Utilization
and Escapement in the Susitna River Study Request
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Track the locations and behavior of
radio-tagged fish using an array of fixed-
station receivers and mobile-tracking
surveys. Aerial surveys are anticipated to
begin in July and end in early October each
year.
Section 9.7.4.2.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Conduct boat-and ground-based
surveys to locate holding and spawning
salmon to the level of microhabitat use.
Section 9.7.4.2.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Establish an array of fixed-station
receivers at and above Devils Canyon to
monitor the behavior of radio-tagged fish
from approximately early June to October
each year.
Sections 9.5.4.3.2 and 9.7.4.3.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Conduct aerial surveys of the upper
river to locate tagged and other salmon.
Sections 9.5.4.3.2 and 9.7.4.1.5.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Locate spawning and holding
salmon upstream of Devils Canyon.
Section 9.7.4.3.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Based on 2012 pilot study results
use side-scan and/or DIDSON to
determine salmon spawning locations in
turbid water.
Section 9.7.4.3.7.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Compare results from current studies
to historical results that characterized the
relative abundance, locations of spawning
and holding salmon, and use of mainstem,
sidechannel,slough, and tributary habitat
types by adult salmon.
Section 9.7.4.5.NMFS Study Request methodology
substantially incorporated into study plan.
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24
NMFS | Study Request Enclosure No. 5:Adult Salmon Distribution, Abundance, Habitat Utilization
and Escapement in the Susitna River Study Request
Requested Study Methodologies RSP Equivalent AEA Explanation
1.3.6: Identify potential barriers to salmon
spawning habitats by species.
2012 Salmon Escapement and Upper
Susitna River Fish Distribution and Habitat
Study efforts began to address this
objective (Sections 9.5.6 and 9.7.4).
Additional data will be collected during
2013 and 2014 pursuant to Sections 9.12.1
and 9.9.4.
NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Determine flows needed for salmon
access to tributaries and mainstem
spawning habitats (e.g., sloughs and side
channels).
Sections 9.12.4 and 8.5.4.6.1.2.3.NMFS Study Request methodology
substantially incorporated into study plan.
1.3.6: Estimate the available spawning
habitat for all salmon species (Chinook,
coho, chum,pink, and sockeye) in the
mainstem Susitna River in all reaches.
No equivalent methodology in RSP.Although AEA is not quantifying available
habitat, AEA will, through instream flow
modeling, quantify flow-habitat
relationships for spawning habitat and will
address potential project effects to that
habitat. See Section 8.5.
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25
NMFS | Study Request Enclosure No. 6:Susitna River Instream Flow Study Request
NMFS Study Request Enclosure No. 6:
Susitna River Instream Flow Study Request
Study Objectives
Requested Study Objectives RSP Equivalent AEA Explanation
1.3.1: Characterize the natural flow regime
of the Susitna River and tributaries in the
project area from the available U. S.
Geological Survey (USGS) gage records,
flow routing data and models, and other
available data.
Section 8.5.4.4.NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Identify, characterize, and integrate
the timing, quantity and function of
instream flow to riverine processes (Poff et
al. 1996; Bragg et al. 2005; Schmidt et al.
2004; Assani 2007): geomorphology;
floodplain and riparian form and
vegetation; biological cues; water
quality; surface/groundwater exchange;
riverine habitat availability and quality,
etc.
Section 8.5.4.7 and 8.5.4.8.NMFS Study Request objective
substantially incorporated into study plan.
1.3.1: Identify, characterize, and quantify
the seasonal (time) and spatial distribution
of all fish species and life-stages of each
species within the defined habitat
delineations of the Susitna River and
floodplain.
Section 9.6.NMFS Study Request objective
substantially incorporated into study plan.
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ATTACHMENT D
Instream Flow Focus Areas
Revised Study Plan 8.5, pp. 8-145 through 8-156
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REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-145 December 2012 Figure 8.5-11. Map of the Middle Segment of the Susitna River depicting the eight Geomorphic Reaches and locations of proposed Focus Areas. No Focus Areas are proposed for in MR-3 and MR-4 due to safety issues related to sampling within or proximal to Devils Canyon. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-146 December 2012 Figure 8.5-12. Map of the Lower Segment of the Susitna River depicting the six Geomorphic Reaches. Focus Areas have not been identified in this segment but will be considered pending results of open-water flow routing modeling. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-147 December 2012 Figure 8.5-13. Map showing Focus Area 184 that begins at Project River Mile 184.7 and extends upstream to PRM 185.7. The Focus Area is located about 1.4 miles downstream of the proposed Watana Dam site near Tsusena Creek. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-148 December 2012 Figure 8.5-14. Map showing Focus Area 173 beginning at Project River Mile 173.6 and extends upstream to PRM 175.4. This Focus Area is near Stephan Lake and consists of main channel and a side channel complex. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-149 December 2012 Figure 8.5-15. Map showing Focus Area 171 beginning at Project River Mile 171.6 and extends upstream to PRM 173. This Focus Area is near Stephan Lake and consists of main channel and a single side channel with vegetated island. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-150 December 2012 Figure 8.5-16. Map showing Focus Area 151 beginning at Project River Mile 151.8 and extends upstream to PRM 152.3. This single main channel Focus Area is at the Portage Creek confluence. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-151 December 2012 Figure 8.5-17. Map showing Focus Area 144 beginning at Project River Mile 144.4 and extends upstream to PRM 145.7. This Focus Area is located about 2.3 miles upstream of Indian River and includes Side Channel 21 and Slough 21. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-152 December 2012 Figure 8.5-18. Map showing Focus Area 141 beginning at Project River Mile 141.8 and extends upstream to PRM 143.4. This Focus Area includes the Indian River confluence and a range of main channel and off-channel habitats. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-153 December 2012 Figure 8.5-19. Map showing Focus Area 138 beginning at Project River Mile 138.7 and extends upstream to PRM 140. This Focus Area is near Gold Creek and consists of a complex of side channel, side slough and upland slough habitats including Upper Side Channel 11 and Slough 11. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-154 December 2012 Figure 8.5-20. Map showing Focus Area 128 beginning at Project River Mile 128.1 and extends upstream to PRM 129.7. This Focus Area consists of side channel, side slough and tributary confluence habitat features including Skull Creek. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-155 December 2012 Figure 8.5-21. Map showing Focus Area 115 beginning at Project River Mile 115.3 and extends upstream to PRM 116.5. This Focus Area is located about 0.6 miles downstream of Lane Creek and consists of side channel and upland slough habitats including Slough 6A. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
REVISED STUDY PLAN Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8-156 December 2012 Figure 8.5-22. Map showing Focus Area 104 beginning at Project River Mile 104.8 and extends upstream to PRM 106. This Focus Area covers the diverse range of habitats in the Whiskers Slough complex. 20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM
Document Content(s)
AEA Response to FERC 12-31-12 RSP Letter.PDF..........................1-9
Attachment A - AEA Proposed Schedule.PDF..............................10-10
Attachment B - RSP Sections 9.5 9.6 9.8.PDF...........................11-116
Attachment C - USFWS and NMFS Crosswalk Table Excerpts.PDF............117-156
Attachment D - Instream Flow Focus Areas.PDF..........................157-169
20130107-5227 FERC PDF (Unofficial) 1/7/2013 4:53:44 PM